Doctor Eggman (Archie)


 * "Dr. Eggman Robotnik" redirects here. You may have been looking for the Doctor Eggman mainly canon to the games.

Origin and the Giant Borg
Robo-Robotnik's early history was largely the same as his Mobius Prime's counterpart up to a point, though there are minor differences such as Robo-Robotnik roboticizing his universe's version of Colin Kintobor. (StH: #92, #197)



The main difference in Robo-Robotnik and Robotnik Prime's history occurred after Robo-Robotnik managed to defeat his reality's version of the Freedom Fighters. Instead of killing them however, he transformed each of them into cyborgs with half robotic-half biological faces. This proved a mistake when the cyborg Freedom Fighters retained their sentience and rampaged through Robotropolis. In a last-ditch effort to save himself, Robotnik turned his own roboticizer on himself, becoming Robo-Robotnik. So dangerous was Robo-Robotnik that he wiped out the resistance and forced Cyborg Sonic to flee from his native zone to seek help from Sonic Prime. Robo-Robotnik soon dispatched a small army of his Shadow-Swatbots to Mobius Prime to destroy all the various Sonics, who had gathered there to discuss how to deal with Robo-Robotnik. However, Robotnik Prime simply dispatched his own SWATbots and destroyed the Shadow-Swatbot army, forcing Robo-Robotnik to temporarily retreat. (StH: #19)

As Robotnik Prime speculated, Robo-Robotnik then went after a piece of the alien Giant Borg suit, the Giant Hand, which was hidden in the Neutral Zone. The Giant Borg, if assembled, had the ability to destroy all the various versions of Sonic and Robotnik. Robo-Robotnik hired the only Sonic from the multiverse not working with Sonic Prime, Evil Sonic, to retrieve the Giant Hand so that he could finish reassembling the Giant Borg. Evil Sonic managed to retrieve the hand before the other Sonics could, and Robo-Robotnik managed to put together to Borg's pieces. He then set out attacking all the various Sonics, but ultimately the Giant Borg was destroyed when every Sonic in the multiverse joined forces and took it apart. Robo-Robotnik was left dismembered from this, his robotic head malfunctioning. His head was hastily brought back to his home zone by Cyborg Sonic. (StH: #19)

Unbeknown to anyone, he survived by transferring his digital mind to a derelict space station in an alternate future reality, where he remained in stasis. (StH: #19, #22)
 * Some argue that the version of Robo-Robotnik seen in StH #22 is not the same Robo-Robotnik in StH #19, as the two seem to have different histories. However, because Robo-Robotnik himself explained they were the same in StH #75, it is considered canon by this site's policy, despite writer Ian Flynn stating he believes there to be two Robo-Robotniks. This may change if the subject is ever revisited.

Near Defeat and Total Victory
What seemed like years later to Robo-Robotnik, Robotnik Prime was accidentally transported by his renegade creation E.V.E. onto the space station in the future reality 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. (StH: #22)

The meeting inspired Robo-Robotnik to fight on, and when he transported Robotnik Prime home, he learned that the Giant Borg's pieces had been distributed throughout the various zones. Locating the piece hidden in that future reality, Robo-Robotnik proceeded to create a new artificial body for himself. He then bombarded Mobotropolis with nuclear weapons, wiping out the Royal Family and the Freedom Fighters, securing his total victory in that zone. (StH: #75)

With all of his enemies killed in his 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. (StH: #75)

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 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 a autobiography on the life of Dr. Robotnik over King Max's speech. (StH: #62, #64, #67, #68, #70, #71, #72)

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 deciding 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. (SSS: #10)

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 personal slave labor force. (StH: #73, #74)

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. (StH: #74, #75)

Birth of Doctor 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 robotic body, which was hidden half a mile below Robotropolis. With his new body, 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. (StH: #75, #76, #77)

After clearing the entire memory bank of all infected data, Eggman discovered a digital file the late Robotnik Prime had 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, Dr. Eggman 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. (StH: #78, #79)

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 Eggman falling into the flooded city below. After Perfect Chaos' defeat by Super Sonic, Knuckles and Tikal, Dr. Eggman demanded revenge, and dispatched Silver Sonic II 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 robotic creation. (StH: #83, #84, #85)

Before Eggman returned to Robotropolis, the Acorn Kingdom 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 great-grandfather Professor Gerald. Using his great-grandfather's notes, Dr. Eggman sought about reviving Project Shadow for his own uses. (StH: #88, #89, #98)

Having learned of the Sword of Acorns' ability to restore the Robian's 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. (StH: #89, #90)

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. (StH: #92, #93)

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. (StH: #94, #95, #100)

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 robot 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. (StH: #105)

Due to the reality warping of Chaos Knuckles, Dr. Eggman was able to create a device to bring back the original Dr. Ivo Robotnik. 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 the original Dr. Robotnik could not exist, the Freedom Fighters went along simply to gain access to the device and destroy it. Following this, the original Dr. Robotnik's molecules dispersed forever. (StH: #108)

Body Hopping and De-Roboticized
As a robot, Dr. Eggman maintained his ability to transport his consciousness into new robotic shells. Following the destruction of Robotropolis due to a nuclear strike from Station Square, Dr. Eggman began constructing a new robotic 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 robotic body with a piece of dynamite. (StH: #110, #116)

While stranded in cyberspace, Eggman attracted his system's self-defences, allowing Snively's consciousness to be transported into a new robotic body. 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. (StH: #117)

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. (StH: #118)

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 aquirred territory to the Kingdom. With the help of Sonic and Sally, 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. (StH: #124, #125)

Now unopposed by Sonic the Hedgehog, Eggman seized the opportunity to re-conquer sections of Mobius which were lost after the original Dr. Ivo Robotnik's death, 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 latter being a sentient computer virus which controlled most of the Eggman Empire's systems and robotic armies. (StH: #130)

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 Eggman'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. (StH: #138, #139, #183)

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. (StH: #182)
 * Writer Ian Flynn has stated the intention was that Albion's citizens were captured and sent to the Egg Grapes where they perished.

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 the Hedgehog, 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. (StH: #130, #131, #132, #133)

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 Zone. Learning of his father's capture, Knuckles the Echidna went to Angel Island with Sonic and the Chaotix and successfully rescued Locke with the help of the Dark Legion. However, Dr. 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, Eggman told his 'daughter' Mecha that given the amount of people captured by Hunter and sent to the Egg Grapes, it was a partial victory. (StH: #138, #139, #140, #141)

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. Eggman came to regret his decision when the four survivors launched a rescue mission that foiled his plans and liberated the prisoners. 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. (StH: #175, #176, #177)

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, 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, Eggman withdrew to his bunker with Snively and the recently arrived Dimitri to plan. (StH: #180, #181, #182, #183)

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. (StH: #184)

Sometime later, Eggman sent Metal Sonic 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, Eggman 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 help the Dark Egg Legion. Eggman revealed that he had planted bombs 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. (StH: #191, #192)

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 Eggman told it to locate Sonic, who at the time had been trapped on Moebius. When Metal Sonic teleported itself there without orders, Eggmans began to yell and throw his tools around in a fit of rage. (StH: #195)

Dr. Eggman later created a new weapon called the Egg Phoenix and used it to counterattack the Freedom Fighters'/Chaotix's assualt 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 to make it stall out. 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 Legion for the final battle. (StH: #197, #198)

The day after, Dr. 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 Chaotix then launched an assault on the Eggdome in an attempt to defeat Dr. 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. (StH: #199 SU: #3)

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. Sonic soon gained the upper hand and struck Eggman down by destroying the Egg Tarantula as the evil doctor was ejected from the machine, causing the doctor to lose his mind entirely right after Sonic proclaimed his victory yet again. 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 Eggman. 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. (StH: #200)

Escape from the Eggman Empire
Sometime after Sonic, Monkey Khan, and the Freedom Fighters fail in their attempt to ambush the Eggman Empire, and then nearly fend off the Empire's attack in New Mobotropolis, Snively visits Eggman in his cell in the Detention Level, telling him how the Eggman Empire is succeeding on its goals without him. He also tells Eggman how he is treated "decently for once" and that he "found love" when the Iron Queen took over the Empire. Unable to understand what Snively is telling him, Eggman continues to utter words to himself, such as "they always loved Colin more..." and "hate that hedgehog...". Fustrated by Eggman's inability to hear him, Snively decides to leave the Detention Level, saying to him that "there's no point in gloating when you can't understand me". While continuing to mutter to himself, Eggman suddenly says "Cell block override authority Epsilon-Gamma-Gamma", which causes the door to his cell to unlock. Hearing the sound of his cell unlocking, Snively goes to investigate, and discovers Eggman outside of his cell and has come loose from his straight jacket. When Eggman sees Snively, he grabs him by the colar and pulls him to his face, asking him "What are you doing out here?! Snoo-ping as usual?!", which indicates that Eggman has not regained his sanity. After escaping the Detention Level, Eggman hijacks a machine that he calls the "Tortoise", and uses it to escape New Megaopolis. He eventually encounters Sonic out in the Great Forest, while apparently looking for Knothole under some trees. When Eggman sees Sonic, it takes him a moment to remember who is, and when he does he begins to attack at Sonic wildly with the Tortoise. He is eventually stopped when Tails shows up and disables the Tortoise, which causes him to ask "". As soon as Sonic goes up to Eggman to tell him that "they were done fighting for the day", Eggman punches Sonic in the face and proclaiming his "victory" over Sonic, and loses conciousness afterwards. When confronted by the Iron Queen and the her subordinates (the Dark Egg Leigon and the Yagyu clan), Sonic orders Tails to take Eggman to New Mobotropolis while he fends off the Eggman Empire. The Freedom Fighters arrive soon after Tails accomplishes his task to help Sonic fight the Empire. After the Freedom Fighters retreat back to New Mobotropolis, they decide to place Eggman in a cell, where they hope he will be safe so they can use him as a hostage in order to gain some influence over Eggman's former Sub-Bosses in the future. (StH: #202, #203, #204, #205, #206)

Recovery and Escape
After the Iron Queen took control of NICOLE, transforming her into Iron NICOLE, the Iron Dominion gained control of New Mobotropolis. Sonic, Sally, Tails, and Monkey Khan fled to break up the four houses. Chuck was imprisoned in a cell next to Eggman and the insane Doctor asked how the "Robot-sizer" was coming along, which gave him a cold rebuke from the hedgehog. At the mention of "Eggman", he started 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..." And he put on his glasses again and slowly began regaining his sanity as well as began thinking of why he couldn't beat Sonic. Eventually, he found the answer, leading him to fully recover, and stated to a visiting Snively 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 unforseen variable in any experiment. When Snivley came around, he told his nephew and asked to be released but was refused, Snivley then said that he is finally being treated fairly and that he found love. Eggman retorted that Snivley was not really in love and that he was only using Regina as a stepping stone for his own gain. This caused Snivley to run out with his eyes full of tears while Eggman laughed evilly. After the Iron Dominion was defeated, Snivley panicked, ran to the detention center, freed his uncle, and escaped. They then took a hovercraft and retreated to the Eggdome. Snivley then asked if he had a plan and Eggman replied that he already had a plan in mind.

In Hiding
While in hiding, Dr. Eggman continued work inside his Eggdome, while keeping tabs on his foes. During this time, he was able to restore Lien-Da to a state of "normalcy", restoring her cybernetics and forced Snively to end his relation ship with the Iron Queen. When Sonic, investigating the Eggdome, encountered the beast known as the Krudzu Hybrid Hydra. However, Eggman, in his desire to be the only one to defeat Sonic, sent a robotic hummingbird to destroy it. Soon after, Eggman and Snively entered the Special Zone and confronted the Zone's guardian, Feist, in an attempt to obtain one of the Chaos Emeralds. He shot down Snively and ended up taking the Chaos Emerald when he was given the choice of bringing back either it or Snively. However, he outwitted Feist by using a teleportation device to scoop Snively out.

Return
With Sonic and the Freedom Fighters busy dealing with the returned Ixis Naugus, Eggman used the time to reappear, using his prize to activate his latest weapon - the Eggdome's true form, the Death Egg Mark 2. Appearing over New Mobotropolis, he forced the Freedom Fighters and Naugus to temporarily work together. Inside the ship, Eggman unleashed the Silver Sonic Mark 3 on Sonic and Sally. Annoyed at Sonic wanting to stay and fight Silver Sonic, Sally took off on her own, leading to Eggman aiming a automated gun at Sally and shooting just as he activates the Death Egg's weapon.

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 Buzzbomber 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 sneak 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 robotizer made everything his "robotic slave".

Piloting his Giant Mech, Eggman viciously attacked Sonic, saying he changed the world to stop the hedgehog 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 rushing Sonic under his foot, only to find he survived and had grabbed a broken power cable, using the Chaos energy in it 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. After 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
Eggman found himself pushing the cosmic reboot button to no avail. He screamed to Snively in frustration, but his nephew was unable to give him the answer for the malfunctioning device. He remembers the events of Genesis, and that is was Sonic who reset everything back. He asks him for the status of stage two, and after Snively confirmed him that it was done, Eggman flew off, telling his nephew not to worry about Sonic and Sally, as they cannot stop him this time. Arriving at the main deck where the roboticizer is, he greets Sonic and Sally by explaining to them that the first white flash had indeed reset the world, shaving away the permanent side-effect of the Bem's De-Robotization. He continues by saying that roboticizing mechanical elements make them explode, stating that it will take care of Station Square, G.U.N. and New Mobotropolis. Sonic attacks him in rage, but Eggman sends him his new Metal Sonic, with a damaged Silver Sonic III following behind. Eggman realizes that Sally disappeared and prepares to hunt her down, but Sonic spin-dashes through his Egg Mobile, sending him to the ground. He picks up a gun to defend himself against the hedgehog, and orders Snively to fire the world roboticizer. Not knowing that Nicole and Sally tampered with the device, the whole charge diverts to the main deck, causing an enormous explosion, destroying Metal Sonic and Silver Sonic III, and gravely injuring Eggman and Sonic. This accident makes him think that the world wasn't reset, and he sadly remarks that Sonic survived the blast. He tries to defend himself with a broken pole, but Sonic smashes him to the ground. As the hedgehog continues to mock him, a robot hand appears from the wreckage. While Sonic glances in horror, Eggman laughs maniacally to what is in front of his eyes: a roboticized Sally.

Abilities
Eggman's most well known ability is his masterminded plots and schemes which only fail due to Sonic and his friends. He is a remarkable scientist and engineer, as evidenced by the armies of robots and mechs he's created. Some of them within mere hours. He is an incredibly skilled pilot: able to manipulate many different kinds of his own mechs and robots in difficult battles with Sonic. Eggman used to have the ability to roboticize someone with a single touch, as well as transfer his consciousness between robotic bodies, enabling him to survive "death".

Personality
Being described on several occasions as being many times more evil and nasty than Robotnik Prime, Dr. Eggman has shown himself to be far more prone to toying with his opponents than his Mobius Prime counterpart. As opposed to simply wiping out Knothole from the get-go, Dr. 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, Dr. Eggman responded "Where would the fun in that be?"

Like Robotnik Prime, Dr. 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). When Hunter was capturing Echidnas en masse, a crudely designed Eggman face was seen above each capture. As a matter of fact, the Egg Pawns needed only a mustache to have Eggman's face. Meanwhile, 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's too late. As Snively has openly admitted, "The big guy is losing his marbles".

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 has begun to fall apart mentally, frequently ranting utter nonsense to no one in particular, not bothering to think things through, and suffering sporadic memory loss (He refers to Snively as "Colin" and the Dark Egg Legion as the "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 his own headquarters and everyone in it at the time simply to finally rid himself of Sonic, which Shadow and Rouge both note as proof that Eggman is losing his mind.

As of his defeat by Sonic in their "final battle' the evil doctor has gone completely insane. His last coherent words being "I... HATE... THAT... HEDGEHOG!!!".

Dr. Eggman has been known to show some child-like behavior, sometimes when his plans don't seem to work, which will often result in him out bursting into rage upon certain failures.

Trivia

 * Eggman decending into madness seems similiar to Dr. Robotnik in the Sonic the Comic continuity.
 * One of Eggman's "shells" looked like famous professional wrestler Hulk Hogan.
 * When Eggman escaped from his Eggdome and "tried to find Knothole", he was quoting lines from E.G.G.M.A.N.. Saying things like "I will destroy the blue one you know." and "He is an obstacle that gets in my way."
 * Just as Sonic was destroying the Egg Tarantula, Eggman yelled "I... HATE... THAT... HEDGEHOG!!!". This line is also used repeatedly by Dr. Robotnik in Adventures of Sonic the Hedgehog.