First Robotnik War

The First Robotnik War was a ten-year global conflict in Mobius's recent history between the despotic mad scientist Dr. Ivo Robotnik and the various settlements on Mobius, as well as the guerrilla warfare waged by numerous Freedom Fighter cells. It came to an abrupt end after Snively Robotnik betrayed his uncle and set the Ultimate Annihilator to erase only his DNA. The war resulted in millions being roboticized and conflicts persisted around Mobius even after the war's official end, as remnants of Robotnik's empire continued to exist. After a short period of peace, it was followed by the Second Robotnik War against Dr. Eggman.

Prelude
In the aftermath of the Great War, King Maximillian Acorn made the decision to dismantle the War Ministry and to appoint Julian Kintobor (The future Dr. Robotnik) as Minister of Science. Unknown to Max, Julian planed to overthrow him. At first, Julian planned to use an army of cyborgs to take control of the Kingdom of Acorn but his only successful subject was Monkey Khan, for the rest had died. To remedy this mistake, Julian sabotaged the original Roboticizer and forced Sir Charles Hedgehog to give him the device. With his plan formed, Julian enlisted the aid of his nephew Snively and prepared to take control of the kingdom. (StH: #43, #72, #79, #86)

The Coup

 * See also: Robotnik's Coup d'état

Spreading Influence and the Freedom Fighters emerge
After believing he secured his hold over what was once the Kingdom of Acorn, Robotnik began to traverse Mobius looking for new areas he could control and establishing Sub-Bosses wherever he could. Among the more notable regions was the Dragon Kingdom (the homeland of his failed experimental cyborg, Monkey Khan). It was here that he endorsed a local warlord known as Jun Kun and his Overlander Magitek sorceress Regina Ferrum with weapons needed to gain the upper hand over the free people and Ninja Clans resisting them, establishing the Iron Dominion. (StH: #207)

Although successful in taking control over Mobotropolis and rechristening the city Robotropolis, Dr. Robotnik had the problem in the form of the Original Freedom Fighters. This group, led by Col. Tig Stripe led guerilla strikes on his city and lured out his robotic army into the Great Forest to destroy them. In time, the fighters became more and more of a greater threat to his regime. Robotnik then bribed Trey Scales into betraying his comrades, who lured them to Robotropolis into a trap. Revealing Trey's betrayal, Robotnik then roboticized the entire group and proceeded to send them all, (Including Scales) into the Zone of Silence. (StH: #142, #143)

In time, he had conquered most of Mobius, leaving only a select few escaping his expanding reach. He then placed his regional governors to maintain lead campaigns against other local resistance movements. (TMS: #1, #2)

However, inspired by the original Freedom Fighters, a resistance group known as the Knothole Freedom Fighters took up the fight against Robotnik. Led by Princess Sally Acorn and the one who would become Robotnik's greatest enemy: Sonic the Hedgehog. (StH: #143, OSM: #0, SSS: #5)

Battle Against Robotnik
Dr. Robotnik would launch several plans in his attempts to destroy the Knothole Freedom Fighters. These plots included using the robotic-plant Krudzu to spread and destroy the Great Forest, creating the "Versatile Evolvanoid" E.V.E. to destroy Sonic, the use of the Weather Annihilator to flush out any resistance, using an amnesia-ridden Sonic to betray his friends, the use of Combots to locate Knothole, and sending supplies to Crocbot in Downunda to quell the local Freedom Fighter cell. All of these attempts proved futile however. (StH: #1, #21, #26, #27, #28, #34, TMS: #3)

Turning Points
At one point, Robotnik nearly managed to achieve victory over Sonic and the Knothole Freedom Fighters. With the help of escaped convict Nack the Weasel, Robotnik managed to capture and roboticize his nemesis, making him the powerful and subservient Mecha Sonic. While Mecha Sonic managed to destroy a large portion of Knothole Village, he was prevented from providing its location when Mecha Knuckles attacked him. Ultimately, Robotnik's plan backfired when the two Robians collided into Robotropolis, turning it into nuclear slag. Sonic was restored to his organic self shortly afterwards by his One Billionth Power Ring, while Knuckles used the de-roboticizer. (StH: #39, SMM)

Following the Mecha Sonic disaster, Robotnik set to work on his next big scheme - the Death Egg; a powerful, orbital battle station capable of roboticizing the entire planet. Robotnik boarded his vessel upon its completion, leaving the rebuilding of Robotropolis to his nephew Snively, who instead used the SWATbot labour force to pamper him. Although nearly successful in sinking the Floating Island, the Death Egg was ultimtely destroyed by Sonic and Tails. (SQM: #1, #2, #3)

After suffering numerous setbacks, Robotnik was furious. He finally developed his ultimate scheme, Operation: EndGame. (StH: #50)

Robotnik's Death; Mobian Victory
Operation: EndGame entailed several phases of the Doctor's greatest plan. Firstly, Robotnik tried to have Sally killed and frame Sonic for her murder, with help from the traitor Drago Wolf. Robotnik would then infiltrate Knothole using a robot replica of King Acorn. (StH: #47, #48)

With Knothole's location now known, the doctor arrived at the Freedom Fighters' doorstep and held them at gunpoint. Rather than kill all of them immediately, Robotnik decided to make his victory more symbolic by using Knothole as a testing ground for his new "Ultimate Annihilator", a satellite weapon capable of warping reality and erasing matter. However, his plan began to unravel when Drago was discovered to be a double-agent and Sonic no longer charged with Sally's murder. Sonic went to fight Robotnik face to face to avenge Sally, but Robotnik managed to fire the Ultimate Annihilator anyways. (StH: #49, #50, SSS: #6)

However, unbeknownst to him, Snively had altered to weapon's programming to only target Robotnik's DNA, which would allow Snively to take over. Robotnik was subsequently erased by his own weapon during his battle with Sonic. (StH: #47, #48, #49, #50)

Aftermath

 * See also: Second Robotnik War

In the immediate aftermath of Robotnik's death, Sonic learned that Sally was actually alive and that she was in a coma. He then implored her to awaken and proceeded to bring her out of her coma with a kiss. The two then celebrated their ultimate victory with the death of Dr. Robotnik. (StH: #51, SSS]: #6)