Doctor Eggman (Pre-Super Genesis Wave)


 * Robo-Robotnik" redirects here. For the version of this character after the Super Genesis Wave, see Doctor Eggman (Archie).

Dr. Ivo Robotnik (born day 253, 3189), also known as Dr. Eggman and early on as Robo-Robotnik V2.0, is the main antagonist of the Sonic the Hedgehog and its spin-off comic series' published by Archie Comics. He is an alternate timeline version of Robotnik Prime with whom he shared much of the same history. The point where they differed was that while Robotnik Prime was destroyed by his own Ultimate Annihilator, Eggman subjected himself to Roboticization in a last-ditch effort to defeat the Freedom Fighters of his world. Though he failed, an encounter with Robotnik Prime inspired him to strike back, annihilating the House of Acorn and many other inhabitants of his world. Thus left with no enemies to destroy, he traveled to Mobius Prime to fill the void left by the demise of Robotnik Prime. He swiftly took on a new appearance and became an even more dangerous threat than his predecessor.

Appearance
Originally Eggman was near identical to Robotnik Prime save the black/blue appearance due to being roboticized. After the loss of his first robotic body, he settled for a more streamlined design. Tall even for an Overlander, Eggman remained obese but became somewhat burlier and less flabby with long, almost disproportionately thin arms and legs. His head is now round as opposed to pointy adorned with both tinted glasses and goggles, and his moustache greatly grew in length, density and mass. Gone are the cape and overlord outfit, in it's place an elegant, red coat sporting two square metal buttons on both sides of the chest in gold with white stripes and yellow cuffs on the sleeves with white gloves covering his hands, and a pair of black pants with matching boots seemingly attached to them bearing circular plates on the both sides of the ankles and three square ones riding up the shin. It was later revealed that behind his pince-nez glasses were the same black eyes with red irises of his original flesh and blood form.

During Operation: Clean Sweep, Eggman wore the same costume he had in the earlier Sonic the Hedgehog games - a red shirt/jacket with yellow triangles (which can be described as either a collar or part of a cape, which can be seen on his back), with black pants with connected boots. He continues to wear his mirrored pince-nez sunglasses.

Origins and initial defeat

 * Main article: Dr. Ivo Robotnik - Early life to Demise

Robo-Robotnik V2.0's early history was largely the same as his Mobius Prime counterpart's, including his jealousy at Colin for receiving more attention from their parents, accomplishments during the Great War, his coup d'état to take over the Kingdom of Acorn, meeting with Ixis Naugus and his war against the people of Mobius. There are some minor differences however, such as Robo-Robotnik roboticizing his universe's version of Colin Kintobor "earlier on", though it is unsure when or where that happened.

The main difference in Robo-Robotnik v2.0 and Robotnik Prime's history occurred on day 46 in the year 3232, as while Robotnik Prime was destroyed by his Ultimate Annihilator, Robo-Robotnik roboticized himself, in order to defeat the Freedom Fighters. This effort proved unsuccessful, and his body was destroyed in the seemingly final confrontation. In reality, Robo-Robotnik managed to transport his digital consciousness to an incomplete and derelict space station he had created for other purposes. Despite his survival, Robo-Robotnik remained stranded on this space station, awaiting inevitable shutdown.

A second chance and victory
Years later, Robotnik Prime was inadvertently transported by his renegade creation E.V.E. to Robo-Robotnik's future reality onto the space station Robo-Robotnik's consciousness was stranded on. Once there, Robo-Robotnik appeared on a monitor and explained that the space station was still incomplete, keeping him mired in space until its systems ran down, which would ultimately end his existence. In response, Robotnik Prime convinced him that even if they failed in this zone, by sending him back to his own zone, they both still stood a chance. Following this, he returned Robotnik Prime to Mobius Prime.

The meeting inspired Robo-Robotnik to fight on, and when he transported Robotnik Prime home, he tapped into his memories and learned about the Giant Borg (which was controlled by an alternative version of himself) and that pieces of it had been distributed throughout the various zones of the multiverse. Locating the piece hidden in his own future reality, Robo-Robotnik proceeded to create a new artificial body for himself with the piece. He then bombarded Mobotropolis with nuclear weapons, wiping out King Sonic, Queen Sally, Princess Sonia, Prince Manik, and the Freedom Fighters, securing his total victory in that zone.

With all of his enemies killed in his native zone, Robo-Robotnik found himself with nothing to do. After discovering the death of his Mobius Prime counterpart, he decided to take advantage of the death of his "other self" by moving to Mobius Prime and wiping out his enemies there, "filling the void" in both his life and Sonic's.

Conspiring from the Shadows
Robo-Robotnik proceeded to conspire from the shadows for several months onboard a group of satellites he brought with him from his own zone. He used each satellite to cause a series of events on the planet surface, first to open the jail cells in the Devil's Gulag prison to release Snively, the Fearsome Foursome, Drago Wolf and Sleuth "Doggy" Dawg, then to cause an avalanche in the Southern Tundra, which nearly buried Sonic and Tails. Following this he activated a series of traps and robots by the Lost Temple of Shazamazon, restored Kodos Lion and Uma Arachnis to their organic selves, hurled a series of meteorites at Mobotropolis, activated a giant Mutate which attacked and captured Snively, fired a time beam at Knothole which could have destroyed all time, and presented an autobiography on the life of Dr. Robotnik over King Max's speech.

Shortly afterward, Robo-Robotnik recruited Evil Sonic to go to the other various realities and have the local versions of Sonic hand over their pieces of the Giant Borg in order to reassemble the machine. Evil Sonic succeeded in doing this, but while in the Sonic Underground universe, the last one to give up its piece of the Giant Borg, Evil Sonic confused the local Robotnik for Robo-Robotnik, and gave him control of the Giant Borg. Because of this, Robo-Robotnik decided he should "cut my losses and forgo the battle-suit", returning to his secret satellites in Mobius Prime for his upcoming scheme to re-take Mobotropolis.

After returning to Mobius Prime, Robo-Robotnik used his satellites to remove the Robians' free will, making them subservient to him. He then had them abandon Knothole and begin working on board his space station. When the Freedom Fighters realized the Robians were absent, they discovered the satellites in space with help from Nicole. Realizing they were likely responsible for the numerous problems which had occurred over the past few weeks, the Knothole Freedom Fighters went to investigate the space stations. Once they arrived on board Robo-Robotnik, wearing a skin disguise to fool everyone into thinking he was Robotnik Prime back from the dead, revealed himself and his use of the Robians as his slave labor force.

After his skin disguise was removed by acid, Robo-Robotnik captured the heroes in a force field, and explained he deliberately lured Sonic and the Freedom Fighters to his space station, as it allowed his Shadowbots to re-capture Mobotropolis. Freed from the force field by Snively, the Freedom Fighters enlisted his help to blow up the orbital platform with Robo-Robotnik on board. Although Robo-Robotnik managed to deport the Robians to the recaptured and rechristened city of Robotropolis, he was prevented from leaving the space station himself when Sonic attacked him. Sonic's attacks proved futile against his robotic body, but soon Sonic's parents revealed they managed to maintain their free will, and were quickly taken by Sonic to the last escape ship. Stranded on board the space station, Robo-Robotnik's body was destroyed along with the station when it exploded.

Birth of Dr. Eggman and early schemes
Despite his robotic body being destroyed in the explosion along with the space stations, Robo-Robotnik simply transported his consciousness into a new, more-advanced body, which was hidden half a mile below Robotropolis. With his new form, he took on the new name: Dr. Eggman. With the city of Robotropolis recaptured, Eggman attempted to download the location of Knothole and launch an immediate attack. However, Sally, NICOLE and Snively successfully planted a virus in the city's computer systems, preventing him from downloading its location.

After clearing the entire memory bank of all infected data, Eggman discovered a digital file his previous self had been researching, regarding the mysterious water beast Chaos. Eggman decided to use Chaos to destroy his enemies. After breaking the Black Emerald and releasing a weak Chaos, Robotnik and a contingent of Shadowbots flew to Angel Island and attacked the Chaos Chamber, shattering the Master Emerald and using its pieces to make Chaos stronger, while also causing the island to fall into the ocean.

Although Eggman managed to aid in allowing the water creature to evolve into Perfect Chaos, the creature decided it no longer would listen to the dictator's orders, and thus destroyed his Egg Carrier sending the doctor falling into the flooded city below. After Perfect Chaos' defeat by Super Sonic, Knuckles and Tikal, Dr. Eggman demanded revenge, and dispatched Silver Sonic v2.0 to Station Square to kill Sonic. After a brief battle however, Silver Sonic II was defeated and reprogrammed by Nate Morgan to act as the city's defender. Thus, when Eggman returned, he was chased out of the city by his own creation.

Before Eggman returned to Robotropolis, the Royal Army and Knothole Freedom Fighters launched an attack on the city, freeing the captured Elias Acorn and obtaining the means to bring Queen Alicia back to health. During this time, Dr. Eggman found himself chased out of Station Square, only to stumble upon the lab and diary of his grandfather Professor Gerald. Using Gerald's notes, Robotnik sought about reviving Project Shadow for his own uses.

Having learned of the Sword of Acorns' ability to restore the Robians' free will, having witnessed it occur on the video files of the Mobian's attack on his city, Dr. Eggman focused his efforts on obtaining the sword. Although he managed to do this, it was stolen from him by Uma Arachnis and given to Kodos.

Weeks later, Eggman discovered a large group of Overlanders, including the Mobius Prime version of his brother Colin Kintobor and his family, had returned to Mobius from a trek through outer space. Having missed his people for so long, and wanting to roboticize this version of his brother, as he had done in his own universe before coming to Mobius Prime, Dr. Eggman created a ruse in order to win the Overlanders trust and lure them into Robotropolis.

Roboticizing with a Touch
Still existing in a robotic body, Dr. Eggman enlisted the help of his nephew Snively to enable his body to roboticize beings with a single touch. The two set to work, and after weeks of experimenting the process was successfully tested on the Overlander Cheddermund. With this new ability, Eggman hoped to roboticize Sonic and the others by luring them into the city using Nate Morgan as bait. Although the Freedom Fighters went to Robotropolis and managed to restore the free will of the Robians there using the Sword of Acorns, which was given to Sally by Uma Arachnis, they managed to escape the city when Nate turned off the city's dome shield. Having remained behind, Dr. Eggman roboticized Nate, turning him into a robotic statue as he had done to Cheddermund.

When Hope pointed out she felt Dr. Eggman was responsible for the Robians, he proceeded to inform the Overlanders they were all suffering from radiation poisoning, and needed to be roboticized or they would die. When Colin learned that Dr. Eggman was a machine and had convinced Snively to help him, Dr. Eggman roboticized Colin as well as Lady Agnes, hoping to also roboticize Hope Kintobor with them. Hope was rescued before she could be captured however by Sonic the Hedgehog. Soon afterward, Eggman demonstrated to the Overlanders they could retain their mobility as long as they wanted to be roboticized, by roboticizing a willing Snively. However, the Overlanders decided to leave the city with the Freedom Fighters, as the Mobians pointed out Dr. Eggman waited for them to get radiation poisoning until it was too late. The Overlanders were allowed to leave, as Eggman felt watching their suffering would be more enjoyable.

Due to the reality warping of Chaos Knuckles, Dr. Eggman was able to create a device to bring back his former self. The two mad scientists then schemed to lure the Knothole Freedom Fighters into Robotropolis and use the same device to disperse their molecules. However, having learned from Dr. Quack that without the device Robotnik Prime could not exist, the Freedom Fighters went along simply to gain access to the device and destroy it. Following this, Robotnik Prime's molecules dispersed forever.

Body hopping and de-roboticized
As a robot, Dr. Eggman maintained his ability to transport his consciousness into new android shells. Following the destruction of Robotropolis due to a nuclear strike from Station Square, Eggman began constructing a new body for himself in the ruins of Old Megaopolis, though this was detected by Station Square's spy agent Rouge the Bat. When Rouge went missing, the President hired Sonic and Bunnie Rabbot to investigate. Bunnie freed Rouge while Sonic destroyed Eggman's new body with a piece of dynamite.

While stranded in cyberspace, Eggman attracted his system's self-defenses, allowing Snively's consciousness to be transported into a new form, first. After Snively made a new look for himself, Eggman destroyed the body and emerged in his new robotic form, telling Snively he was the main villain. In this form, Dr. Eggman traveled to the Forbidden Zone where the Fearsome Foursome, Sleuth "Doggy" Dawg and Drago Wolf offered to sell him back one of his old factories. Dr. Eggman agreed in order to shake Drago's hand and roboticize him, as well as roboticizing the Fearsome Foursome. Before he could roboticize Sleuth however, Sleuth informed him he would give him Sonic the Hedgehog, who traveled to the Forbidden Zone to rescue his childhood friend Tommy Turtle. Sonic managed to grab Tommy from Sleuth and nearly escape, causing Eggman to switch his attention to Sleuth and roboticize him. Just before he did however, Sleuth threw a grenade which destroyed Eggman and Snively's robotic bodies, and caused Sonic to think Tommy had died in the explosion.

Shortly after this encounter, Eggman found himself captured along with Snively, Sonic and Tails by an alien race known as the Bem. Eggman and Snively were transformed back into flesh and blood, and forced to battle for their lives against a roboticized Sonic and Tails in order to prove whether or not flesh is superior to metal. After losing to Mecha Sonic and Mecha Tails, both Eggman and Snively were sent back to Mobius in their organic forms. Additionally, they are unable to re-roboticize themselves due to a side-effect of the Bem's de-roboticizer.

The Xorda crisis and re-conquering Mobius
Not long after this, Mobius was attacked by another alien race called the Xorda. The Xorda had attacked Mobius over twelve thousand years ago when the planet was still known as "Earth", and had thought all intelligent life had been wiped out. When the Xorda encountered ships carrying Overlanders, the descendants of humans, they returned to Mobius to find the planet still inhabited. When the Xorda attack Eggman's forces, he realized the Xorda posed a legitimate threat, and asked for an alliance with the Kingdom of Knothole, but at the price of surrendering half of the his acquired territory to the Kingdom. With the help of Sonic and Sally Acorn, the Xorda ship was forced to retreat. Unwilling to leave the job unfinished, the Xorda left behind a device called the Quantum Dial intended to destroy the world and the entire solar system. Sonic successfully prevented the device from going off, but was teleported to another side of the universe in the process, leaving everyone to believe he died.

Now unopposed by Sonic the Hedgehog, Eggman seized the opportunity to re-conquer sections of Mobius which were lost after his predecessor's demise, thereby creating the Eggman Empire Establishing a new capital city for his empire in New Megaopolis outside the ruins of Old Megaopolis and Megaopolis, Dr. Eggman also went about creating two robotic "children" to replace the still-missing Snively, who disappeared during the Xorda's attack, called Mecha and A.D.A.M.,the former as his bodyguard and the latter being a sentient computer virus which controlled most of the Eggman Empire's systems and robotic armies.

Dr. Eggman also took this time to strike a deal with the Dingo Regime, providing weapons and other support for them in return for their allegiance and becoming his enforcers on Angel Island. With the Dingoes now an ally and under the new leadership of Kage Von Stryker, he successfully conquered the Angel Island and maintained control of it for months, enslaving most of the Echidna population. During a bid to captured the Master Emerald, the Brotherhood of Guardians managed to defeat Robotnik's Egg Pawns, but were captured in their weakened state by Dr. Finitevus, leaving the echidnas and Master Emerald under the sole protection of Locke until the Dark Legion chose to aid him. Eggman would also ally with the Iron Dominion like his alternate self did.

In addition to taking over the echidna settlement on Angel Island, Dr. Eggman sent in his forces to invade the hidden city of Albion, having its location provided to him by Dr. Finitevus who also sabotaged the city's defenses. With the city defenseless, Eggman's forces destroyed the city, and its citizens sent to the Egg Grapes where they perished. In another attempt to control Downunda, Eggman established the first Dark Egg Legion chapter with former Freedom Fighter Duck Bill Platypus as its Grandmaster. He would go on to establish other chapters, including one in the southern continent under Drago Wolf and Razorklaw, though the name Dark Egg Legion would not apply until the Echidna chapter joined the Eggman Empire.

When Sonic returned months later, Dr. Eggman decided to initiate Operation: Triple Threat; a nuclear strike against Station Square and Knothole, while also sending a horde of upgraded SWATbots to take down the force field containing the nuclear radiation around the nuked Robotropolis. The horde was intercepted at Fort Acorn by the Mes Braves Battalion, the Chaotix and an expeditionary force from G.U.N. while the Knothole Freedom Fighters attacked Dr. Eggman and his battleship armed with the nukes. Eggman managed to escape from Shadow, who arrived as well to stop the mad doctor's schemes, but the nukes were delayed from launching when Tails occupied A.D.A.M.'s thought process, giving Bunnie Rabbot the time she needed to destroy the battle ship. He would later learn that several former Robians had been "Re-Roboticized", apparently by a being calling himself Anonymous. At the same time, an Auto Automaton operation of his involving Tommy Turtle was under way, but foiled by the efforts of the Freedom Fighters.

Shortly after this failure, Dr. Eggman sent in his forces to invade Golden Hive Colony, capturing or killing most of its citizens and turning it into one of the Eggman Empire's polluting bases. It was also around this time that Locke had been captured while holding off Dingo forces while the Dark Legion relocate the Master Emerald to the Hidden Palace. Learning of his father's capture, Knuckles went to Angel Island with Sonic and the Chaotix and successfully rescued Locke with the help of the Dark Legion. However, Eggman, not wanting to rely on the Dingoes, sent his new agent Hunter to capture some of the free echidnas as well as retrieve the Master Emerald. Hunter successfully sent numerous echidnas to the Egg Grape Chambers including Remington, but was soon defeated when Knuckles transformed into Super Knuckles and sent Hunter flying off the island to his death. Rather than think of it as a loss, Robotnik told his 'daughter' Mecha that given the amount of people captured by Hunter and sent to the Egg Grapes, it was a partial victory.

Eggman later introduced a new army of robots to the top threats to his empire, including Sonic, Tails, Knuckles, and Amy. Later, after discovering Freedom Fighter activity near an abandoned bunker, the doctor would create a new Metal Sonic to investigate. His robot would engage Sonic, Shadow, and a prehistoric robot named Isaac in battle, though the robot would form a truce with his fellow automaton and learn about Mobius' history from him before being destroyed. Later, frustrated with his efforts to conquer Mobius, Eggman unwittingly gave A.D.A.M. clearance to utilize nanites in their efforts, having developed the technology in creating his new Metal Sonic.

Some time later, after developing a vehement hatred for Mina Mongoose's music, which led him to ban it in his territories, he hired Nack the Weasel to assassinate her. After that failed, he dispatched new versions of Heavy and Bomb to eliminate her, only for that to meet with failure as well. His next scheme involved sending an army of Robian Dragon to the city of Vesuvio after learning its location from Dulcy the Dragon, who then helped destroy his forces. Anonymous would then send him a warning that he was to be terminated, and Eggman decided to go to Sonic for help; they were then forced to deal with the threat of a reprogrammed Mecha and Knothole's hijacked Metal Sonic Troopers. At the same time, he was able to convince Shadow to join him as an agent of the empire in exchange for knowledge about his past. He was then surprised to learn that A.D.A.M. had contact with nanites seized by the Freedom Fighters, allowing them to infect Nicole, Jules Hedgehog, and Bunnie Rabbot.

Continuing his vendetta against Sonic, Eggman dispatched three agents against Freedom HQ on Sonic's birthday: Bark the Polar Bear, Bean the Dynamite, and Croctobot, all of whom were subsequently defeated. Then, as he prepared to use the Egg Grapes in his efforts to mine the Zone of Silence for energy, the Egg Grape Chamber was invaded by the Arachne, who utilized the Sword of Acorns and forced him to evacuate. Upon returning, he found the Grapes gone and his old foe Ixis Naugus escaped. The wizard then departed in search of the Crown of Acorns, and Eggman then destroyed Mecha after receiving footage from A.D.A.M. that showed her working with Anonymous. After terminating all his other "henchmen" projects, leaving only A.D.A.M., he deployed the Egg Fleet to capture not only Naugus' force but also Mammoth Mogul and the Destructix, who had joined forces to battle the Freedom Fighters and Chaotix.

After capturing Jet the Hawk, leader of the Babylon Rouges, Eggman decided to hire him and his associates to attack Knothole and humiliate Sonic, though their use of Extreme Gear was countered by Tails' creations. The doctor had also by this point established-or else would later establish-loose ties with the Battle Bird Armada, an organization that the Babylon Rogues had deserted for their own purposes. Robotnik also convinced Snively to rejoin the empire as commander of the Egg Fleet. The doctor subsequently set up an Auto Automaton Infiltrators operation in Casinopolis under Renfield T. Rodent, but was thwarted by the Chaotix.

Not long after that, he revealed to A.D.A.M. that he had discovered his "son" was in fact Anonymous, having witnessed him release Mammoth Mogul and Ixis Naugus from the Egg Grapes and learned of his involvement in Anonymous' plots. He then deleted A.D.A.M., only for the virus to return by taking over the nanites infused into Tommy Turtle's shell. Eggman was then taken to the nanite city, where A.D.A.M. faked his communication signal to bring in Shadow, who had been dispatched after Mogul and Naugus. Eggman then watched as Jules, under the control of A.D.A.M.'s nanites, brought him Tails. Eggman remotely summoned the Egg Fleet, which A.D.A.M. revealed he had detected, and then watched as A.D.A.M activated the Summmoning Spire, using Tails and Shadow's respective powers to draw in the Chaos Emeralds from across Mobius and all over the galaxy. After Sonic arrived and began engaging A.D.A.M., eventually leading to a battle between their super forms, Eggman freed both Super Shadow and Turbo Tails, who sent the Emeralds to another zone. Tommy was then able to override A.D.A.M.'s control of the nanites fused to his body long enough to open himself to fire from the Egg Fleet upon Dr. Eggman's orders before departing.

Shadow himself soon betrayed Eggman, stealing Gerald Robotnik's diary and deserting the Empire to pursue his own destiny. Eggman was then able to capture Sonic and use a special device to control his actions and have him attack Knothole, but was defeated in both this attack and dispatching yet another Metal Sonic model by the combined efforts of Sonic's friends. Following this setback, Eggman sent Nack, Bark, and Bean to investigate a supposed auction of the Master Emerald, but all three were captured. He also suffered defeat in attacking the old Power Ring Grotto and the Chao who had taken up residence there, as Sonic, Knuckles, and Tails intervened. However, his plans continued to move forward, and he even caught Espio the Chameleon as the Chaotix member invaded his headquarters, gaining a measure of revenge for Espio's role in destroying his captured Golden Hive Colony holdings.

Dr. Eggman then launched a large-scale offensive against the Kingdom of Knothole, using his massive Egg Fleet to inflict heavy damage via aerial bombardment, effectively destroying the entire Kingdom and Freedom HQ. During this attack, he managed to capture the entire population (bar Sonic, Tails, Knuckles and Amy), transporting them to his Egg Grape Chambers to be used as a source of fuel for his city. He also engaged in a one-on-one duel versus Sonic wearing his newly created power armor called the Egg Beater, thrashing Sonic physically and psychologically before he departed. Robotnik came to regret his decision when the four survivors launched a rescue mission that foiled his plans and liberated the prisoners, but not before the doctor briefly subjected Charmy Bee to the Egg Grapes, causing memory impairment. The Mobians were subsequently transported to New Mobotropolis when Nicole altered the programming of the Egg Beater to transport them there, as opposed to the Egg Grape Chambers. In retaliation, he redeployed his Egg Fleet (lead by Snively) to attack the city's shield while he fought Sonic in his Egg Beater. The combined might of Sonic, the Freedom Fighters and the Chaotix proved too much for his power armor, resulting in its destruction and causing Eggman to flee, slowly losing his grip on reality as well.

Turning of the Tides
When Dr. Eggman learned of the return of Enerjak, he accepted Sonic's proposed temporary alliance so that the two could defeat the chaos demigod. Arriving at New Mobotropolis during Enerjak's attack there, he successfully had the Egg Fleet transport him to the last Egg Grape Chamber. Keeping his end of the bargain, Eggman withdrew from New Mobotropolis with the captured Enerjak, saying he wanted the place kept tidy for when he decided to return and destroy it. However, in his arrogance Dr. Eggman underestimated Enerjak's power, and was shocked when the demigod escaped captivity and destroyed not only his Egg Fleet but the vast majority of New Megaopolis. Following this, Robotnik withdrew to the Eggdome with Snively and the recently arrived Dimitri to plan.

Following the defeat of Enerjak, Eggman accepted an alliance proposed by Lien-Da for the remaining Echidnas loyal to her to become the new Dark Egg Legion in exchange for robotic enhancements. Eggman agreed knowing that he'd already given the title of Grandmaster to Dimitri, despite Lien-Da only allying under the terms that she would be the Grandmaster.

Sometime later, Eggman sent another Metal Sonic model to attack Freedom HQ, only to discover that it was under the control of Scourge the Hedgehog and the Suppression Squad. Metal Sonic was just about to leave when Eggman heard Scourge say he was planning to take control of the areas that the Eggman Empire had conquered, causing him to have Metal Sonic attack Scourge. When Sonic arrived, Robotnik realized that Metal Sonic was outnumbered and built a duplicate of Scourge, Metal Scourge, to help. While the doctor was watching the battle from the Eggdome in New Megaopolis, Dimitri came to him and demanded to know why he had not yet built a new Badnik army to supplement the Dark Egg Legion. Eggman revealed that he had planted explosive devices in the cybernetics of the Legion's members, causing Dimitri to realize just what he had gotten himself into and leave. Eggman presumably continued to watch the fight between the two hedgehogs and his robot duplicates until the latter were both destroyed.

However, this did not discourage the good doctor, who proceeded to construct yet another Metal Sonic. This newer version was equipped with a special engine which would allow it to travel to other dimensions. Upon activation Dr. Eggman told it to locate Sonic, who at the time had been trapped on Moebius. When Metal Sonic teleported itself there without orders, Eggman began to yell and throw his tools around in a fit of rage.

Eggman later created a new weapon called the Egg Phoenix and used it to counterattack the Freedom Fighter/Chaotix's assault on the Eggdome. The Egg Phoenix proved to be a match for the two groups, but Sally came up with the plan of having Sonic, Vector, Knuckles, Tails and Bunnie use teamwork to lead the Egg Phoenix straight up into the air, stalling out its engines. With the fires out on the Egg Phoenix, Saffron, Charmy and Ray planted Neutralizing Mines on the craft's hull allowing Tails to deactivate the Egg Phoenix and caused it to crash. Eggman escaped unscathed and ordered Snively and Dimitri to round up the Dark Egg Legion for the "final battle".

The day after, Eggman dispatched the last of the E-100 Series, E-123 Omega to hunt down and destroy the rogue E-102 Gamma, much to Omega's displeasure as his original programming was to destroy Sonic the Hedgehog and not this lower task. The Freedom Fighters and The Chaotix then launched an assault on the Eggdome in an attempt to defeat Eggman once and for all, while the Dark Egg Legion held them back. Secretly following Snively's plan, the legion later retreated to let Sonic get through and even saluted him when he was about to confront Eggman. Sonic then went down the chute where Eggman was waiting in his Egg Tarantula.

Descent into madness
Confronting his rival about how he had conquered the planet, Eggman's sanity was pushed to the breaking point as Sonic taunted and recounted the numerous times he'd defeated the dictator, and a long and grueling battle ensued in which he showed increasing signs of instability. Sonic soon gained the upper hand and struck Eggman down by destroying the Egg Tarantula as the evil doctor was ejected from the machine. Right after Sonic proclaimed his victory yet again it caused the doctor to lose his mind entirely, going as far as to rip his own mustache. Screaming and drooling he made a swing at Sonic, missing and falling to the floor. As Sally walked in on the scene, she found Eggman lying on the ground, now having descended into madness and babbling incoherently. At this point, Snively walked in, remarking how Sonic had not just defeated his uncle, he had "broken" him. Instead of rejoicing at the defeat of their oppressor, Sonic and Sally merely looked with pity and horror at what had become of the once-mighty Robotnik. After the Freedom Fighters left New Megaopolis to celebrate, Snively placed Eggman in a padded cell and handed over control of the Eggman Empire to the Iron Queen and her dominion.

Not too long afterward, Snively and the Iron Queen attacked New Mobotropolis by having the latter use her powers of Magitek on Bunnie D'Coolette and later Monkey Khan, but when Bunnie was taken away from her and Khan was restored to his senses the two fled. Snively went back to the Eggdome and took a look in on Eggman, who was busy mumbling nonsense sentences. Once Snively left him thinking that gloating in his uncle's face a waste of time, Eggman muttered the door's override code, unsealing him from his cell unlocked.

Snively heard the sound, only to see his uncle escape his straitjacket and confront him for "Snooping as usual". Robotnik then tossed Snively aside and rushed off with only one intention: destroying Sonic. Blowing a hole in the dome, he scared away the Yagyu and DEL, ranting as he went into the Great Forest with his Egg-Tortoise, searching for Knothole by tearing up the forest tree by tree. He encountered his target there and after recognizing him attempted to destroy him, but Sonic kept avoiding his attacks. His focus on Sonic made him ignore Tails who eventually shut down the robot from a control panel. Sonic then attempted to reason with Eggman but he just punched the hedgehog. He soon fainted after a fit of laughter at 'getting' the hedgehog.

After the Iron Dominion arrived and demanded that the heroes relinquish custody and surrender themselves, Sonic held them off while Tails dragged the unconscious Eggman back to New Mobotropolis. Once brought back to the city, Monkey Khan wanted to kill Eggman for his atrocities, but Sally convinced him that he was more valuable alive and had him incarcerated in the New Mobotropolis Prison. After forcing the Iron Dominion to retreat (with the help of the Freedom Fighters and Nicole), Sonic visited Eggman in prison, the delusional former dictator being out of touch with reality and thinking that he had just made his defection during the Great War. He then promptly fell asleep in order to rest up for his audience with the king.

Later, during the Iron Dominion's invasion, Eggman was visited by his nephew while scribbling numbers and figures on the walls, his mustache growing back. Confronting his uncle about how pathetic he had become, Snively marched up to Eggman and announced that he would be lording over a greater empire than his had ever been. The speech, however, was useless on the mad doctor who merely asked Snively when he had lost all his hair, completely killing the mood.

Recovery and escape
When his old "friend" Sir Charles was escorted to the detention center, Eggman, in his delusion, asked how his invention the "Robot-sizer" was coming along, only to get a cold rebuke from the aged hedgehog. In a moment of clarity, Eggman reflected on the use of his adopted name, remembering that he used to go by "Julian" but that it had been a long time since he had done so. Studying his glasses he began mumbling: "I go by Robotnik now, and sometimes... "Eggman" ...of my Eggman Empire..." With that, he put his glasses back on, seemingly regaining some semblance of his lost sanity and began thinking over why he could never defeat Sonic.

Eventually, he found the answer which lead him to make a near full recovery. During a visit from Snively, he explained that the reason he could never defeat Sonic was due to the hedgehog's over exposure to Chaos energy, making him the embodiment of chaos, an unforeseen variable in any experiment. He then asked him to be released from his cell, however Snively refused, stating he had everything he wanted, including love. After learning Snively's "love" was Regina Ferrum, Eggman laughed, declaring him a deluded fool who could never find love since he only cared for himself, while the woman he supposedly loved was merely a stepping stone to him in his goal for conquest who would play him as easily as Snively would her. This reduced his nephew to tears and he stalked off, Robotnik all the while laughing at him, saying he'd be back to serve him once again. Sure enough, the Iron Dominion was toppled by the efforts of the Freedom Fighters and Regina was captured, leaving a terrified Snively to free his uncle, both of them escaping New Mobotropolis in the confusion.

Hiding and scheming
One week afterward, Eggman had a recovering Lien-Da and the Dark Egg Legion back under his command in the lower levels of the Eggdome, secretly watching Sonic's returns to the site around the bunker, searching for the elusive doctor. Eggman saved Sonic from the Krudzu Hybrid Hydra with a humming bird like robot when it threatened to eliminate Mobius's hero, stating that no one, not even himself was allowed to destroy the hedgehog, much to Snively's annoyance. He continued to gleefully watch Sonic and Tails' failed attempts at finding him and finding safety in numerous surveillance system re-routings, he dismissed Snively's worries of being caught. When Snively suggested that they journey to the Dragon Kingdom to rescue the Iron Queen from jail, the doctor swiftly put his nephew in place and told him flatly, "We're not wasting any of MY time or resources busting YOUR girlfriend out of jail!" Submissively, the tiny Overlander complied as his overbearing uncle petted him like a lapdog. Eggman then set about building more machines, and preparing for his next comeback.

Later on, Eggman had Snively brought to him under watch by armed legionnaires, revealing that he was aware of Snively contacting the Dragon Kingdom. Defending himself, Snively claimed he had been sending supplies off to the Dragon Kingdom to legionize the Raiju Clan to make them the regional enforcers. In response, the despot demanded his nephew to officially end his relationship with Regina, immediately. Brought nearly to tears, Snively reluctantly complied while silently vowing otherwise.

During this whole time, Eggman also supervised Lien-Da's recovery while installing more cybernetics and upgrades into her and making her look almost completely natural using his skill. After installing a replacement explosive, he showed her what he had done and explained it as all being part of a game he played with Snively and his Grandmasters to see how far the "trust" of each other would benefit them, to which Lien-Da accepted gladly.

Dr. Eggman and his loyal minions continued to work on completing repairs to the Eggdome for quite some time. While he was informed by Lien-Da that all systems were up and running, and that the hull damage had been repaired, Eggman told Snively to meet him at the Zone Gate. Afterwards, Eggman took Snively with him to the Special Zone through the newly constructed portal and encountered Feist. Faced with a literal god, the two overlanders were subjected to one of Feist's games to prove themselves worthy of the prize. Racing against each other through a tube, Robotnik shot Snively's craft down and claimed victory. Feist then gave him the choice between bringing Snively, or the emerald back. Unsurprisingly, Eggman chose the gem and promptly returned to the Eggdome where he activated a teleportation device to bring Snively back as well, much to the panda's otherworldly fury.

Reemergence
Putting the new "battery" in place within the Eggdome's core, the doctor met up with his lieutenants on the command deck where he was pleased to find that all systems were online and the engines ready for take off. After initiating the countdown Eggman gleefully watched on as his masterpiece charged up, the launch procedure reducing the surrounding ruins to a further state of decay, until the Death Egg Mark 2 finally blasted off and headed straight for New Mobotropolis.

The Death Egg's presence was impossible for the Mobians not to take notice, which was what Eggman counted on as he waited for the enemy to make their move while "Operation: Clean Sweep" charged. As Snively made him aware of an attacker inbound, Eggman unconcernedly assumed it was the rodent as usual, only to be thoroughly shocked at the grinning visage of his old enemy Ixis Naugus on one of the surveillance screens. Quickly gathering himself again, Robotnik was pleased to find the internal Power Ring matrix was resisting Naugus' magic, as well as that Sonic on the offensive, and ordered his forces to aim at the hedgehog's friends instead. After Sonic and Sally managed to get inside, he promptly left the command deck to have some fun despite protests from his lieutenants. Guiding the heroes to where he wanted, Eggman then unleashed his latest Silver Sonic-model on them. While Sonic clashed with the considerably improved robot hedgehog Robotnik taunted Sally, all out thanking her and the Acorn family for allowing him to rise to such a position of power. His mocking was interrupted by Snively who reported that the weapon was fully charged and ready for firing. Brushing his nephew's concerns aside, he activated the device with a toast to his victory as the world was enveloped in a white light...

Genesis
During the Genesis event, Robotnik spent his time capturing and placing small animals inside robotic shells for his Badnik Army in preparation of global conquest. After his nephew reported back to him about an incident, Doctor Eggman decided to investigate himself. Finding a group of Mobians in the Marble Zone, he recognized the blue one as the one who had bullied his nephew and opened fire on Sonic after a brief exchange of words. As the rodent avoided his weaponry, Eggman eventually cornered him on a pillar in a lava field. Gleefully preparing to finish the hedgehog off, the doctor was attacked by a reprogrammed Badnik which he swiftly eradicated, only to leave himself open to a direct and critical hit from Sonic. With his Egg Mobile severely damaged and spewing smoke, the scientist retreated while shouting threats of his master plan, despite not being entirely certain of all the details of it himself.

Eggman escaped to the Scrap Brain Zone where he waited for the Freedom Fighters. When they came, he trapped Sonic in a force field near some elevator shafts and then attacked him with balls of electricity. Before he could do anything else though, Antoine fell through a hydraulics pipe and into his arms. In the distraction, Sonic smashed the pipe elevator he was sitting in and Eggman hid in another pipe elevator as Sonic was freed from the force field. Unluckily for the doctor, Sonic caught him as he tried to sneek away and smashed his Egg Mobile, causing him to fall into a pit below.

Eggmn survived the fall however, and returned to the Death Egg to check up on his plans. Like Snively, he did not seem to remember well the effects of "Phase 1" to his scheme, but stated "Phase 2" to be a global one-shot "robotization" after the Death Egg was fully recharged with the seven Chaos Emeralds in their possession. He then brushed off his nephew's concern about the dimensional disturbances, saying that he would soon win and proceeded to work on a "logic puzzle", referring to Sonic.

Eggman returned to the planet and went to the Metropolis Zone, awaiting for Sonic in his Egg Mobile. Once the hedgehog arrived, he congratulated the "Rodent" for coming this far, this time causing a memory reaction in Sonic. This annoyed Eggman greatly, not wanting it to go further, and he deployed replicas to attack Sonic. Midway through the battle, all power across the zone shut down due to the actions of the Freedom Fighters in Oil Ocean Zone. Eggman then fled to the Death Egg in a shuttle with Sonic grabbing on in hot pursuit. Aboard the battle station, Eggman confirmed to Sonic that the world was falling apart, but would be "cemented" once the Death Egg's roboticizer made everything his "robotic slave". Piloting his Egg Destroyer Battlesuit, Eggman viciously attacked Sonic, saying he changed the world to stop him from interfering with his plans like always. With Sonic all but beaten, the doctor then made the mistake of telling him the Death Egg was powered by the Chaos Emeralds right before crushing Sonic under his foot, only to find he survived by using the Chaos energy in a broken power cable to become Super Sonic. Incredulous that the hedgehog still lived, Eggman was infuriated as all his attack were trumped and had no effect on Sonic. As Snively attempted to warn him the planet was beyond saving, Super Sonic slammed his Mech into a wall with Eggman cursing him while he used Chaos Control to undo the reality warp, washing the world again in white...

Return To Roboticizing
In the restored world Eggman found himself pushing the Cosmic Reset Button to no avail and screamed at Snively in frustration as his nephew was unable to explain why the device would not work. The doctor suddenly remembered the events of the first time with Sonic setting everything back and asked Snively for the status of "Stage Two". After Snively confirmed it was ready, Eggman made his way to the lower decks and told him not to worry as he could not be stopped this time. Arriving in the world Roboticizer's chamber, Eggman greeted Sonic and Sally and explained to them the first white flash had indeed reset the world, removing the permanent effect of the Bem's De-Roboticization. Robotnik continued by saying that even if the immunity still held, roboticizing mechanical elements made them explode, which enabled him to destroy all of the United Federation, G.U.N. and New Mobotropolis in one move. Sonic tried to attack Eggman in a rage, but the doctor had his newest Metal Sonic intercept the rodent, with a damaged Silver Sonic v3.0 following behind.

Eggman then noticed Sally disappeared and armed his Egg Mobile to hunt her down, but Sonic spin-dashed through it, sending him to the floor. As he picked up a gun to defend himself against the hedgehog, Robotnik ordered Snively to fire the world roboticizer. Unaware that Nicole and Sally tampered with the device, the beam inverted to the chamber, causing an enormous explosion which destroyed the Sonic robots, and severely wounded the Death Egg. Eggman survived the blast believing from the accident that the world was not reset, and resignedly found Sonic to be alive too. He then tried to defend himself with a broken pole, but Sonic smashed him to the ground, and declared victory over Eggman yet again. As the hedgehog continued to mock him, a robot hand appeared from the wreckage and while Sonic stared in horror, the battered Robotnik laughed in maniacal delight at the sight before him: a roboticized Sally.

Despite his injuries and the loss of the world roboticizer Eggman was satisfied with the prospect of having a robotic minion Sonic could n0t bring himself to fight. Toying with the idea of having Mecha Sally march both herself and Sonic into an incinerator the doctor decided instead that he wanted to enjoy this delightful turn of events and had her literally throw the hedgehog out along with the trash. Complimenting his new minion on a job well done Robotnik ordered Snively to prepare for an all out assault on New Mobotropolis only to have his nephew inform him that the Chaos Emerald was gone and that the Death Egg was running low on power. Furious at having the "Chaos Factor" against him again Eggman ordered a full retreat and the dual launch of project Titan and project Deadly Cuddles as he headed for the command deck with Mecha Sally. While his Egg Legionnaires frantically tried to stabilize the Death Egg with what little power they had left Eggman opted to use it for the Egg Annihilator Beam despite a protest from Snively that was swiftly quenched by his latest addition to the Death Egg's staff. The assault, however potent, was foiled by a now crystallized Titan Metal Sonic and without any power to spare, the doctor and his forces were forced to flee.

While his nephew updated him on their current state with the damaged Death Egg and missing Chaos Emerald Eggman promptly ignored him as the doctor preoccupied himself with something far more intresting, namely checking up his newly acquired enemy-turned-minion. Growing annoyed with Snively's sniveling over the lack of power, damages and missing "battery" Eggman menacingly informed his lackey that the Egg Mites would handle the repairs, while he had prepared numerous refueling depots long before even thinking about using the Chaos Emerald as a power source. The distracted dictator then merrily told him to relax and get out as he continued to work on the princess, vowing to make the most of her current state.

Shortly after, Eggman was contacted mystically by Ixis Naugus, who told him of the Freedom Fighter's plans to relocate ex-king Elias Acorn from New Mobotropolis to his old home in Feral Forest. The next day, Eggman attacked Elias and the Freedom Fighters, using his new, upgraded soldiers, a rebuilt Metal Sonic, and Mecha Sally. He watched gleefully as the Freedom Fighters were overpowered. Following his recent patterns, he settled for a lesser victory by commanding Metal Sonic to self-destruct while latched on to Antoine. Mecha Sally returned to the Death Egg and they retreated, leaving Elias alive and Antoine barely alive.

Betrayed...Again
After quietly scheming, Snively tried to throw the Eggman Empire into disarray by broadcasting a message that Eggman had been killed and the Empire was done. He locked Eggman out from the systems and fled the Death Egg to gather Hope and join Regina. Eggman activated Orbot and Cubot to help him regain control and to act as his new lackeys. He transported the Dark Egg Legion's leaders to the Death Egg to reveal that he was alive and to give the order to capture Snively if possible and to be on the lookout for the missing Chaos Emerald. He revealed his latest project, another Metal Sonic, Mecha Sally (which he promoted he roboticized himself), and the new Metal Knuckles and Metal Tails. Later, he took Orbot and Cubot with him on a ship to chase after Snively, who had left the tracking systems open.

Tracking his wayward lackey to Central City, Eggman continued the hunt in his usual subtly and launched a full scale attack on the city with an army of Egg SWATs and three large mechs to smoke him out. Aboard his Egg Camel the doctor (repeatedly) tried to agitate Grandmaster Hugo, whom Eggman had brought along to show him the nation he once protected at the mercy of the Eggman Empire. But the brainwashed cyborg soldier responded with a monotone Yes, Sir, at every turn, much to Eggman's disappointment. After a fairly one-sided battle between the imperial forces against Omega and the defending G.U.N troops Eggman noticed Snively making an escape and recalled all units from the battlefield to pursue him, allowing the clearly outmatched Federation to claim "victory" as he left.

Making his way through Yurashia in search of Snively, Eggman soon reached Stormtop Village and proceeded to sack it with his robot army. After some resistance in the form of his other wayward minion Eggman unleashed his new main enforcer on Monkey Khan who couldn't bring himself to harm her. Flanked by Orbot and Cubot, Eggman decided to do a little terrorizing on the villagers unless they told him where to find the imprisoned Iron Queen, which they told him right away to his disappointment. Questioning his former vassal about the whereabouts of his tenaciously treacherous nephew, Regina was predictably less than pleased with the good doctor's visit and none too helpful. Interrupted in mid-conversation by Khan who had managed to drain Mecha Sally's power and desperately told him to give her a new battery Eggman gleefully replied that she ran on Power Rings, and pointed out that his crown was the only substitute to the monkey. While his revived minion restrained Khan after he gave her his crown Eggman presented him with a control crown to replace it and smugly summarized the spoils of the day. Then Snively arrived on the scene, seated on the towering Iron Oni's shoulder. After tearing Regina's entire prison cell/well from the ground and loudly declaring his defiance of Eggman right in the doctor's face, Snively turned the Iron Oni on his uncle at Regina's request. Undeterred, Eggman told his former minions that he hadn't even begun fighting yet.

Towering over his uncle with the Iron Oni, Snively, declared the Eggman Empire his and threatened to destroy his former leader once and for all. Eggman however sent Orbot obtain a robot to combat Snively while he himself remained and stalled, trading banter and insults back and forth with his nephew. Finally, after Snively was considerably riled up by Eggman's allegations that his relationship with Regina was an illusion, Eggman summoned the mind-controlled Khan and had him attack the Iron Oni, only for Regina to use her Technomancy and transform the simian into Iron Khan, who then entered battle with Mecha Sally while Eggman himself frantically fled from the approaching Iron Oni. With his Egg-Swat guards distracting Snively Eggman found Orbot and Cubot (who hadn't selected a robot, much to Eggman's chagrin) and summoned a robot himself—the Egg Beater, which was immune to Regina's magic. Eggman commandeered the robot and entered battle with Snively, and after sustaining a small amount of damage succeeded in grabbing the Iron Oni and preventing it from attacking. Receiving an omni-tool from Orbot, Eggman proceeded to sabotage the Oni, cutting power lines and shifting its internal balance. A simple push afterward was enough to destroy the entire Iron Oni, leaving Snively and Regina unconscious. Eggman loaded up the two in a Prison Egg, boarded his Egg Mobile and retrieved Mecha Sally from Khan (who had been freed from Regina's control) without hassle, allowing Khan an opportunity to rescue the village as well.

Later Regina awoke in the Prison Egg, finding herself in the Dark Egg Legion's base in the United Federation territory, and Eggman explained to her that he should have believed her and Snively's romance from the beginning, which would've saved him a great deal of trouble. He then snapped his fingers and summoned Snively, who hugged Regina and the two thanked him for his mercy. Appointing the two Grandmasters (and demoting Hugo Brass), Eggman left after informing them that he expected them to play his "game" along with the rest of his minions. Later still, Eggman taunted the real Snively outside the latter's Prison Egg cell, explaining that not only did he defeat Snively, he also increased his authority over the D.E.L., defeated G.U.N., terrorized some Mobians, and even learned the location of Hope Kintobor so he could single her out. Finally, Eggman revealed that the "Snively" he left in the U.F. D.E.L. base was in reality a robotic Infiltrator-one created by Snively himself-and that Regina was unlikely to discover the ruse any time soon. Adding that the real Snively was going to stay in the Prison Egg for the rest of his life, Eggman left his former lackey to rot.

Pursued by Team Fighters
By now, victory seemed within Dr. Eggman's grasp at last: he had even more control over the Dark Egg Legion than ever before, the Freedom Fighters had disbanded, the Republic of Acorn was led by a hostile government, and his treacherous nephew could no longer undermine him. At some point after Snively's capture, Eggman invaded Furville with the intent to roboticize and/or legionize the population; the last thing he needed was any new heroes with the Freedom Fighters supposedly broken. However, as his forces, led by Mecha Sally, began terrorizing the city and abducting the citizens, his victory was cut short by arrival of Sonic and Team Fighters; his longtime enemies had not given up despite everything, and even worse, they had overcome the psychological impact of Mecha Sally. Having underestimating his enemies once again, Eggman called for a full retreat to restock and refuel---and to think of his next strategy.

Arriving in Soumerca, Eggman tried to incite war between the Felidae and the Wolf Pack by having Mecha Sally kidnap Lupe and Hathor, hoping to buy himself time. After Queen Hathor escaped, Eggman decided to legionize Lupe, since the wolves were among those still immunized to roboticization. However, Team Fighters tracked him down and were guided by the escaped Hathor to the Death Egg. Tails secretly planted a tracker on the Death Egg while Lupe was rescued. Eggman hastily ordered a retreat, unaware of the tracker which would allow Team Fighters to follow him wherever he went.

Despite the Death Egg still being fairly low on resources, Eggman decided to try and attack New Mobotropolis again. He stopped at Feral Forest first, hoping to have Mecha Sally kill the desposed Elias; even if she failed, the attack would hopefully keep Team Fighters distracted long enough for him to carry out his attack. Tails Doll disabled the city's shield, and the invasion commenced. However, the combined efforts of Team Freedom and another group, the Secret Freedom Fighters, thwarted the assault. Eggman was so enraged that he could barely retain his sanity; Sonic was not even present in the city and still he had failed to conquer it. He was forced to order yet another retreat, with Team Fighters resuming pursuit.

Desperate to lose Team Fighters, Eggman tried to stall them by first setting a Titan Metal Sonic possessed by Krudzu Hybrid Hydra on them, then attacking Albion. To make sure they stayed off his trail, he left Lien-Da, her contingent of the DEL, and Metal Knuckles in Albion, threatening the Grandmaster with dire consequences if she failed him. In the meantime, Eggman set his course for the Northern Tundra.

During this period, the Chaos Emerald that went missing upon the failure of Operation: Clean Sweep was found by another mad scientist, Dr. Wily, the arch-nemesis of Mega Man, in his world. In attempting to examine the gem, Wily accidentally interrupted Eggman as he was berating his Grandmasters for their failure to find the Emerald. The two doctors briefly argued before Eggman realized that something beneficial could come from their meeting. After explaining about alternate realities to Wily, Eggman came up with an idea on how to eliminate both Sonic and Mega Man. Meeting up in the Skull Egg Zone, a pocket zone constructed by the Doctors, the two got to work on constructing their collaborative air fortress, the Wily Egg.

With his plan with Wily almost ready for activation, Eggman briefly returned to the Prime Zone, where the Death Egg had just docked at the Northern Tundra. Upon his return, he learned of Shard and sent a new Metal Sonic, equipped with a free will algorithim and power gem, to eliminate him; Metal Sonic succeeded, but was forced to self-destruct in the process. Eggman quickly rebuilt a new model, which retained it's predecessor's memories and free will, and sent it to the Skull Egg Zone.

Shortly thereafter, Team Fighters arrived in the Northern Tundra and invaded the Death Egg with the Arctic Freedom Fighters and Silver the Hedgehog. Eggman, completely at his wits' end with Team Fighters by this point, furiously ordered Mecha Sally and several Egg Swats to destroy the invaders, but Mecha Sally was defeated and subdued by Silver. Facing almost certain defeat, Eggman retreated to the Skull Egg Zone, where Wily was waiting for him. Safe from being directly effected, the doctors set off a second Genesis Wave: once again resetting the Prime Zone, and for the first time, Wily's dimension, Earth 20XX.

Two-Universe Tyrant

 * Note: Due to the Genesis Wave, Eggman's history from this point were changed to be nearly identical to that of his game counterpart's.

With the Prime Zone completely changed, and Earth 20XX skipped forward in time, the doctors began the next phase of their plan, beginning by sending Metal Sonic and Bass to kidnap Tails, and having the young fox Roboticized in the first ever Roboticized Master, Tails Man. Bass and Metal Sonic were deployed to capture other friends of Sonic's, and in no time the doctors commanded a force that included Rose Woman, Shadow Man, and Knuckles Man. While using their Roboticized Masters to collect the Chaos Emeralds for their ultimate plan, Eggman and Wily set about pitting their respective enemies against each other in an effort to buy time. They accomplished this by having Metal Sonic interfere in Mega Man's attempts to stop the first four Roboticized Masters from stealing a Chaos Emerald from the Mega City bank, while having Copy Robot attack Silver the Hedgehog in view of Sonic. Luring the pair to the same area of the Green Hill Zone, they watched eagerly as their respective nemeses did battle while Tails Man relayed footage to them. However, their celebration was interrupted when a Warp Ring opened to allow Mega Man to take the battle back to his world. Realizing that his old rival Dr. Light-whom he had neglected to tell Eggman about-must be responsible, Wily agreed with Eggman's assessment that he be dealt with. Metal Sonic and Bass volunteered to take on the task, and headed out for Light Labs.

As the fight continued in Mega City, Sonic and Mega Man started to converse and realize that things were amiss. Terrified that they would figure out the truth and join forces, Eggman ordered Tails Man to attack them, and after some convincing Wily agreed. Much to their horror, the attack not only failed, but resulted in Tails Man being restored to his organic form by the combination of Sonic and Mega Man's abilities. However, all was not lost, as Metal Sonic and Bass succeeded in capturing Dr. Light and bringing him to the Wily Egg. Sonic, Mega Man, Tails, and Mega Man's allies Rush and Proto Man soon entered the Skull Egg Zone in pursuit, and Wily dispatched the Copy Robot and Genesis Unit to stop them. Eggman remained unimpressed with Wily's developments, and annoyed his partner with claims that he contributed more to their team. After Silver Man and Blaze Woman arrived with the final Emerald, the two agreed on a contest: whichever one of their nemeses managed to survived longest would demonstrate the superiority of their representative world. Accordingly, they challenged the victorious heroes with their full remaining compliment of Roboticized Masters: Tails Man's three former teammates, the duo who collected the final Emerald, and the trio of Vector Man, Espio Man, and Charmy Man.

The doctors watched gleefully as their eight minions attacked Sonic and Mega Man's team, only for Proto Man to break off to start a solo search for Dr. Light. Fearing the threat Dr. Light might pose if freed, Eggman ordered everyone but the former Chaotix to pursue Proto Man. The remaining trio continued to attack Sonic and Mega Man's party until they, like Tails Man before them, were restored to organic form. Eggman was frustrated by this development, but Dr. Wily surprised him with confidence. The doctors agreed to dispatch both their Robian Shadow Man and the Robot Master Shadow Man against the heroes, and then prepared to build a new shared mecha for their eventual confrontation with the heroes. Eggman questioned his partner's surprising attitude, and was informed that Mega Man's successes had previously come to his receiving aid from Dr. Light, something that was impossible with Light as their prisoner. The two visited the captive Light to gloat over his capture, only for Eggman's henchmen Orbot and Cubot to arrive and inform them of the defeat of the Shadow Men. Silver Man and Blaze Woman were next to be dispatched to attack the heroes, but they were restored as well.

Left with only two Roboticized Masters, both Eggman and Wily put on a brave show, but Eggman secretly planned to betray Wily and take the Wily Egg back to Mobius in the event that he was thwarted. Still, they began preparing their remaining defenses, including the Robot Master Army. Knuckles Man and Rose Woman were dispatched to attack Sonic's party as well with orders to self-destruct if necessary to destroy the heroes, but they were restored to living form as well. As the doctors concentrated on completing their Egg-Wily Machine X, they began disagreeing over the configuration, only to be informed that the Wily Egg had been sabotaged and Bass and Metal Sonic were in pursuit. The doctors headed to their location and arrived just in time to see spy Rouge the Bat release their Chaos Devil, who helped subdue her before being ordered back into confinement. Confident in the success of their creation, they ordered Rouge's Roboticization and went to prepare for the coming assault of the heroes.

While their Robot Master Army and Rouge Woman engaged Sonic's allies-including the former Roboticized Masters-Eggman and Wily decided to torment Light again by sicking a Motobug and a Met on him. However, the two minion robots ran into each other and destroyed on another, much to the doctors' humiliation. Light took advantage of the moment to try and sway Eggman and Wily from their evil path, reminding them of previous times when they had tampered with greater forces only to lose control. Wily was left unnerved, but Eggman found himself wondering how Dr. Light knew so much about him and their plans. The two left Light in his cell and went to observe the ongoing battle, but Eggman later returned with Metal Sonic after Orbot picked up a signal coming from the cell. Discovering Light attempting to communicate with a device cobbled together from Motobug and Met parts, Eggman revealed that he had deduced that Light had been conspiring against them with Rouge. He then had Metal Sonic throw Dr. Light out of a nearby airlock towards certain death.

Dr. Light survived the attempt on his life, but Eggman and Wily's good-natured partnership did not: Wily proved furious after seeing Eggman's attempt to kill his former rival. Retaining their alliance but treating each other coldly, the pair dispatched the Mega Man Killers, Chaos Devil, and the trio of Bass, Metal Sonic, and Treble to counter Sonic and Mega Man's intrusion into the Wily Egg. However, Eggman determined that Wily had proven himself too soft, and vowed to eliminate him. The two went to work completing the Egg-Wily Machine X, despite the fact that Duo-an ally of Mega Man's who came to his and Sonic's aid-and the Chaos Devil were threatening to tear the Wily Egg apart with their battle. Eggman warned Wily that the disruption of their Genesis Reactor could destroy both their universes, and encouraged him to concentrate on finishing their vehicle. The two managed to complete the Egg-Wily Machine X shortly before Sonic and Mega Man defeated their final defenders, and then attacked the two heroes and captured them. They then informed them of their ultimate plan: to use the power of all seven Chaos Emeralds to rewrite both their universes without limit.

Overjoyed at the prospect of ruling their universes without opposition, Eggman and Wily briefly regained their old enthusiasm but then remembered their existing rift. It became worse when Sonic's attempts to convince Eggman to give up his course prompted Eggman to reveal that his and Wily's efforts in reshaping reality threatened the existence of both their worlds, angering Wily further. Eggman calmed him by assuring him that the Super Genesis Wave they would soon launch would repair all damage to reality. However, the pair were then attacked by Proto Man and Knuckles, forcing them to retreat to their machine. In attempting to defend themselves, each attempted to activate their personal defenses, only to discover that each doctor had sabotaged the other. Reluctantly cooperating in order to survive, they managed to repair the Egg-Wily Machine X and empower it with energy from the Chaos Emeralds. Sadistically informing Wily that he would kill him when it was all over and getting the same in kind, Eggman set his sights on the red heroes only to confront another menace: their freed nemeses transformed into Super Sonic and Super Armor Mega Man. An intense battle resulted between the doctors and their super-powered enemies, which resulted in the defeat of Eggman and Wily. As the two heroes prepared to undo the Super Genesis Wave and its predecessor, Wily accepted the situation, but Eggman refused to and launched what remained of the Egg-Wily Machine X to attack Super Sonic. His efforts broke Super Sonic's concentration, and he also launched an attack right as Sonic unleashed the energy that would have restored their world.
 * Note: From this point, Eggman's history continues from his new life in the altered timeline.

Personality
Being stated on several occasions as being many times more nasty and evil than the original Robotnik ever was, Eggman has shown himself to be far more prone to toying with his opponents than his Mobius Prime counterpart on numerous occasions. As opposed to simply wiping out Knothole from the get-go, Eggman decided to "have fun" with his Mobian enemies and take the time and resources to engage in "war-games". Eventually he grew tired of this, and decided to use the Mobians as a source of fuel for his capital city via the Egg Grape Chambers. When his mechanical "daughter" Mecha asked if there wasn't a far more efficient and easier method to powering his city, Eggman responded with a nonchalant ''"Where would the fun in that be?" ''

Like Robotnik, Eggman is also arrogant, and egotistical, both of which may be his greatest weaknesses. He has a habit of frequently putting "Egg" into the names of numerous inventions and places (Egg Fleet, Egg Pawn, Egg Lobster, and Egg Grape Chamber to name a few). He has also stated that Ixis Naugus is the reason why he likes science more than magic.

Despite his genius, Eggman has the annoying habit of thinking that his plans are foolproof, even when the flaws are quite obvious (Metal Scourge done on the fly, Egg Grapes needing retooling for Enerjak, telling Dimitri about the explosives, etc.), and not realizing that there may be a problem until it is too late, and at one point of desperation, he even ordered his Egg Fleet to fire on his enemies while he was standing right next to them without concern for his own well being.

Following the destruction of his entire city, the loss of 99% of his forces, the betrayal and subsequent deaths of his "children", and his never ending litany of defeats at the hands of Sonic and the Freedom Fighters, Eggman began to fall apart mentally, frequently ranting utter nonsense to everyone and no one in particular, not bothering to think things through, and suffering sporadic memory loss (such as when he referred to Snively as "Colin" and the Dark Egg Legion as the "Dark Alliance"). In one instance, he was perfectly willing to use a super-weapon that would destroy not only the Freedom Fighters, but also half of the EggDome and everyone in it at the time, simply to finally get rid of Sonic, which Shadow and Rouge both noted as proof that Eggman was losing all grip on reality (though Sonic refused to believe it until he witnessed the doctor's breakdown with his own eyes). Yet another subsequent defeat at Sonic's hands finally drove Eggman completely insane, up to the point where he was unable to differentiate between events that occurred ten minutes ago from those that occurred ten years ago (for example, he used the Egg Tortoise to search for Knothole long after he himself destroyed it). However, he did experience a moment of clarity while in conversation with an irate Chuck Hedgehog. From thereon, Eggman's senses gradually returned to him.

Shortly before the Iron Dominion's defeat, Eggman had, as Snively put it, "reasoned [himself] back from the brink." After the Dominion's fall and his subsequent return to the EggDome, Eggman had seemingly regained most of his sanity, though still displaying slightly more prominent mood swings than before.

Power and abilities
Eggman was an ingenious and cunning individual whose skill in science and technology seemed unmatched, and he was also a brilliant strategist and schemer, creating numerous underhanded plans that caused the citizens of Mobius much grief and misfortune. Eggman also had the skills for making machines that would cause mass destruction, but his most powerful and cruelest weapon was the nuclear bomb which he used as "Robo-Robotnik" to destroy his original Mobius, which was powerful enough to decimate all life.

Robo-Robotnik used to have the ability to roboticize someone with a single touch after making upgrades to his "Eggman" body. As Robo-Robotnik, Eggman was essentially unkillable due to being able to transfer his mind into other robotic bodies before he could be destroyed, enabling him to survive death countless times, and if a body was too difficult to locate, he would still be able to stay alive within the digital world. However he lost all his robotic abilities after he was turned into an organic being by the Bem.

Allies

 * Dark Egg Legion
 * Grandmasters
 * Lien-Da
 * Duck "Bill" Platypus
 * Drago Wolf
 * Razorklaw
 * Akhlut
 * Beauregard Rabbot
 * Diesel
 * The Foreman
 * Regina Ferrum
 * Bride of Conquering Storm
 * Badnik Horde
 * Metal Series
 * Metal Sonic v3.0
 * E-100 Series (formerly, most units destroyed)
 * Sub-Bosses
 * Iron King (formerly)
 * Crocbot (formerly, destroyed)
 * Octobot (formerly, destroyed)
 * Kage Von Stryker (formerly, deceased)
 * A.D.A.M. (formerly, destroyed)
 * Dr. Wily
 * Wily's Robot Masters
 * Bass

Enemies

 * Freedom Fighters
 * Knothole Freedom Fighters
 * Sonic
 * Tails
 * Sally
 * Bunnie
 * Antoine
 * Rotor
 * Nicole
 * Amy
 * Chaotix
 * Knuckles
 * Wolf Pack
 * Mercian Freedom Fighters
 * Downunda Freedom Fighters
 * G.U.N.
 * Team Dark
 * Shadow
 * Rouge
 * E-123 Omega
 * Silver
 * Blaze
 * Light Labs
 * Dr. Light
 * Mega Man
 * Proto Man

One or two Robo-Robotniks?
Some argue that the version of Robo-Robotnik seen in Sonic the Hedgehog #22 is the same Robo-Robotnik in Sonic the Hedgehog#19 Former writer Ken Penders who wrote both stories confirmed on his website the two were the same person. Additionally Sonic the Hedgehog #75 firmly established that the two were the same Robo-Robotnik, which was solidified by Dr. Eggman's Data File from Sonic the Hedgehog #108. Despite this, current writen Ian Flynn decided to retcon this and made the Robo-Robotnik from Sonic the Hedgehog #22 separate from the one in Sonic the Hedgehog #19. This is a result of the fact that the two seem to have minor differences in their histories and both Robotnik's failed to recognize one another in Sonic the Hedgehog #22. Despite in-comic canon considering the two the same Robo-Robotnik, Ian Flynn's position, reflected in Sonic the Hedgehog: The Complete Sonic Comic Encyclopedia, is the most recent take on their relationship and can as such be considered the current retconned explanation. Ian Flynn's position on the debate was officially printed in the Sonic Free Comic Book Day 2011, where information on Dr. Eggman was presented in the back of the issue.

Trivia

 * Dr. Eggman's current look was introduced to coincide with the version of Robotnik in the Sonic Adventure videogame. Although primarily known as Eggman in the comics, he is sometimes still referred to as Robotnik to prevent newer readers from getting confused.
 * According to Archie Comics employee and Off-Panel artist Jon Gray, Eggman's history as "Robo-Robotnik" is no longer canon to the comic in the new Post-Super Genesis Wave World. This is most likely because the concept was introduced by Ken Penders. Itthus can be assumed that Eggman can now be considered to be the original Prime Zone version of Robotnik.
 * While Eggman's design is, for the most part, identical to his current videogame counterpart's design, the only place where this deviates is his eyes. After his decent into insanity in Sonic the Hedgehog #200, it was revealed Eggman has the same black and red eyes as the original "SatAM" Robotnik. In the rare occasions in which his eyes have been seen in the games however, they've been shown to be ordinary white-sclera eyes, with eye color being shown to be either black (Sonic Advance 3) or blue (Sonic the Hedgehog (2006)).
 * Eggman had other robotic bodies hidden underneath Robotropolis, but it is unknown why he did not use them. All of them have similar features and similarly coloured uniforms. One of them even appeared to be fashioned after the famous wrestler Hulk Hogan. Since Dr. Eggman was meant to resemble his current look in the games, the out of continuity explanation is quite obvious. The explanation in continuity was only hinted in the letters pages and a Q&A held on Ian Flynn's forum, with Eggman thinking his new form looks good. Interestingly enough, Robotnik Prime's first reaction to Eggman's appearance was to call him a "boob". Interestingly enough, Eggman's current body bears a passing resemblance to Gerald Robotnik, it is possible that this was intentional as Eggman looked up to him and possibly based it off of him as a tribute.
 * Many people have noted that Eggman's descent into insanity is similar to that of his Sonic the Comic counterpart.
 * When Dr. Eggman loses his sanity, he uses what the original Dr. Robotnik said each time he was defeated by Sonic, "I HATE THAT HEDGEHOG!". The line "I HATE THAT HEDGEHOG!" was used by the Dr. Robotnik in the Adventures of Sonic the Hedgehog and Sonic the Hedgehog television series.
 * Eggman's line of "Snoo-ping as usual" in Sonic the Hedgehog #205 is a nod to the internet meme Robotnik Pingas, well known among Sonic fans on YouTube. His line "I'm going to be on TV! I'm going to be a TV Star!" is from the same series and gained meme status from a video made by the same user who made the term "Pingas" popular.
 * Eggman makes reference to his theme song from Sonic Adventure 2 called "E.G.G.M.A.N." during his escape from the Eggdome, saying, "I will destroy the blue one, you know! He's the obstacle that always gets in my way!"
 * Although they are usually covered by his moustache, Eggman does have ears.
 * Since Eggman is officially from the future Mobius Nicole came from, his age is to be debated. Either the fact that being roboticized and stocked in a space station stopped his aging factor, either a recton has to be made. If he was roboticized when he was 42 (Day 46, 3232) and trapped on the satellite for at least twenty years (as Queen Sally was shown to still be alive two decades later), then that would make him 62 years of age. If he returned to Mobius Prime later in that year, he would be 63. The year is now 3237, and he has yet to have his birthday, so he can be considered at least 64 now.
 * Many references throughout the series have suggested that nearly everything that happened in the original Dr. Robotnik's life up until "End Game" also happened to Eggman, which is speculated to be the point of divergence in their timelines. This was further solidified when both Eggman and Ixis Naugus both recalled their first meeting together as being exactly the same despite the fact that they both came from two different realities.
 * It is speculated that Robo-Robotnik v2.0's initial defeat might have been self-inflicted. Given how roboticization causes non-organic compounds to combust, his original body could've been very well destroyed during the process. His left arm had already been roboticized prior to the incident and had various built-in cybernetics at the time.
 * Some characters like King Maximillian still refer to Eggman as Robotnik because he has for most of the time in his life been quantitative with Robotnik Prime.
 * Though Eggman does not appear in the Mega Man comic series until "Sonic and Mega Man: When Worlds Collide", he was acknowledged by Doctor Wily as Ivo in Mega Man #23