Doctor Ivo "Eggman" Robotnik (Post-SGW)

Early Life
Dr. Eggman was born as Ivo Robotnik, the grandson of the brilliant scientist Professor Gerald Robotnik. In childhood, Robotnik looked up to his grandfather as a hero, and believed him to be a great man who had done his best to help mankind. Thus the doctor decided to follow in his grandfather's footsteps and became a scientist. However, at some point he became obsessed with the idea of the entire world under his rule, and using his unmatched genius, began his plans.

Early Schemes and Conquests
Robotnik started his career as a technical researcher for the Guardian Units of the Nation. It wasn't long before a fellow coworker of his, Dr. Julian Snively, stumbled across his plans for world domination. Not wanting to let the information slip out, Robotnik bribed him into becoming his chief mechanic.

With help from the royal wizard, Walter Naugus, Dr. Robotnik became the royal adviser of King Acorn, the ruler of the Kingdom of Acorn. He claimed that the United Federation was launching an invasion against the kingdom, but it was all a ruse created by him and Naugus to prepare an army of robots to aid in their takeover of Mobotropolis. Thanks to his "contributions", Robotnik was granted full access to the kingdom's resources, which assisted in his conquest to obtain the Chaos Emeralds and construct his superweapon: the Death Egg. After conquering Mobotropolis, he banished King Acorn and Naugus to the Special Zone, and was able to establish his Eggman Empire.

However, a young Sonic the Hedgehog would begin foiling the plans of Dr. Robotnik (now giving himself the alias "Dr. Eggman"), and later joining him were the group of heroes would later be become known as the Freedom Fighters, who would end his rule over Mobotropolis and soon after free King Acorn. Eggman however had still managed to create a powerful empire for himself and was able to use it to spread his evil ambitions across the globe but would continually come into conflict with his mortal adversaries each time.

An attempt of Eggman's to eliminate Sonic following his loss of Mobotropolis involved the Super Special Sonic Search & Smash Squad and a "captured" Breezie the Hedgehog. Breezie fed information to Eggman that allowed him to deploy robots against Sonic such as the original Silver Sonic. In return, Eggman would reward Breezie in such a way as to insure her financial security. Sonic eventually faced off against Dr. Eggman in the Egg Storm Chamber, where Eggman held Tails captive. However, the Naugus twins, Walter and Wendy, arrived nearby seeking revenge on both Eggman and Sonic. Eggman let Tails go free in an attempt to keep Sonic from chasing after him while Eggman fled before the twins could find him. However, he was intercepted and trapped in crystal by the twins before he could escape, and Sonic caught up with him moments later, only to be trapped in crystal himself by Wendy. Tails, watching from afar, sadly promised to rescue Sonic as the twins walked off with their captives. In the end, the twins were defeated, and both Sonic and Eggman were set free.

Some time after this, his attempts to launch the Death Egg were thwarted time and again by Sonic. This was despite his briefly tricking Knuckles the Echidna, Guardian of Angel Island, and gaining control of the Master Emerald.

Eggman would later hatch a plan to search the Eastwatch Islands for the Ancient Gears in order to run his new super-weapon, the Mega Drive. As he would also need to Master Emerald to power his new weapon, Eggman would once again trick Knuckles, this time into believing Sonic had been going on a rampage as Super Sonic with the Chaos Emeralds. Agreeing to let Eggman watch the Master Emerald, who he had believed had cleaned up his act, Knuckles waited for Sonic to show up at Cascade Temple Zone, one of the Eastwatch Islands, under the orders of Eggman. With the Master Emerald now in his possession, Eggman set about his search for the Ancient Gears. The first one he would find was in Green Seaside Zone, where he encountered Sonic and Tails, who winded up defeating him and retrieving the Ancient Gear along with freeing captured animals, with Eggman fleeing. He would then go on to encounter Sonic, Tails, and Amy in Flower Park Zone, where he lost another Ancient Gear to the heroes as well as more captured animals. Eggman then fled to Cascade Temple Zone, where Knuckles sprung his trap on the heroic trio. After they helped him realize that Eggman had once again tricked him, the four formed a team and encountered and defeated Eggman once again, retrieving another Ancient Gear and saving more captured animals in the process.

After fleeing to Glitter Park Zone, the four heroes once again encountered Eggman, who, despite lying in wait to attack the heroes, was easily defeated thanks to Tails' strategy and the power of Tails, Amy, and Knuckles, with Sonic watching on. After losing another Ancient Gear, the mad doctor fled to Haunted Depths Zone, where he encountered Sonic by himself, who had split up from his group of friends. After losing another battle and another Ancient Gear to his nemesis, Eggman fled to the next island, Eruption Ruin Zone. He reused a version of the trap sprung by Knuckles in Cascade Temple Zone, this time with lava instead of water, but was unable to stop the reunited four heroes. Fleeing on foot to a new machine, Eggman challenged the group once more, but was bested by the combined efforts of Sonic and Knuckles, while Tails and Amy had to take a quick breather from the heat. After losing another Ancient Gear, Metal Sonic who swooped in to steal the five Ancient Gears that Tails had as well as kidnap Amy. Both Eggman and Metal Sonic then fled to Eggman's newest flying fortress. While devising a list of demands in exchange for Amy, Eggman was interrupted by Sonic, Tails, and Knuckles, who had realized where Eggman and Metal Sonic could be hiding. After handing over their Ancient Gear in exchange for Amy thinking that Eggman didn't have the seventh one (since Eggman specifically asked for the "last" Ancient Gear from Sonic after stealing the five from Tails), the team realized that Metal Sonic had the last Ancient Gear inside of it. After the three defeated Metal Sonic and saved Amy, Eggman and Metal Sonic fled to Eggman's deep sea base directly under the fortress, as the airship was only for supply shipments.

Dr. Eggman later launched an operation on Isolated Island that was thwarted by the Chaotix, resulting in numerous Badniks being left on the island. Another creation of his was the computer virus Phage, who despite her abilities apparently disappointed Eggman severely. Her fear of Eggman's wrath later prompted an attempt to retake Isolated Island and Dr. Ellidy's research for Eggman.

At some point in time, Dr. Eggman and his forces invaded Lupe the Wolf's. Sonic the Hedgehog, Sally Acorn and Antoine D'Coolette came to her aid, and Sonic ran off to follow and defeat Dr. Eggman while Antoine defended Sally and Lupe. Using the terrain of the Thunder Plains Zone to his advantage, Sonic lead the evil dictator into a lightning bolt, destroying the doctor's vehicle and sending him fleeing, resulting in an exchange of dialogue where Dr. Eggman expressed his hatred for his blue foe and Sonic made a mockery of his nemesis's name.

At a later point, he was known to have devised a plan involving the water beast Chaos and his flying airship the Egg Carrier, but was stopped by Sonic with the aid of Tikal. Sometime after that, his creation Metal Sonic rebelled against him and became the Metal Overlord, forcing him to rely on the aid of the Chaotix (and later Sonic and his friends) in order to stop it and after its defeat he was able to place a safeguard on Metal Sonic to ensure its continued obedience. Sometime after that, he was caught up in the Black Arms invasion, in which he was one of the many inhabitants of the planet to be rendered immobile by a toxic gas released from the Black Comet. Later, he initiated the first Genesis Wave on the planet, dividing it into pocket dimensions, but eventually Sonic and his friends restored the world to normal. At another time, he created a massive Interstellar Amusement Park in order to take control of other planets and enslave a small race of aliens called Wisp in order to harness their Hyper-go-on power for his Mind Control Cannon, luckily this interstellar invasion plan was put to an end thanks to Sonic and Tails (who also had help from a Wisp named Yacker and Silver the Hedgehog).

The Time Eater and Meeting with Dr. Wily
Dr. Eggman also launched an attempt at conquest using the power of the Time Eater, which he attempted to harness with help from a past version of himself. This effort was thwarted by Sonic and his younger self, and left Eggman stranded in a white void outside time and space. This led to his initial contact with Dr. Albert W. Wily from the alternate reality Earth 20XX, as Dr. Wily, using a Chaos Emerald sent via the Time Eater defeat, had accidentally contacted Dr. Eggman as he was trapped in the white void and proceeded to aid him in escaping. 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, and set off the second Genesis Wave on both their planets.

Worlds Collide
With Sonic's world completely changed, and Mega Man's world shifted 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. Thomas 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 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 universe, causing it to mysteriously shatter.

Countdown to Chaos

 * From a readers perspective, this picks up from where the original pre-Super Genesis Wave continuity left off

Following his disastrous failed attempt to stop Sonic from reverting the Super Genesis Wave, Eggman crash-landed in Efrika, his mind filled with a completely different set of memories of an alternate life. Cursing both his blue nemesis and Dr. Wily, he ordered Orbot and Cubot to drag his Egg Mobile out of the wreckage of the Egg-Wily Machine X. At the same time, Tails Doll attacked Mobotropolis on previous orders due to Walter Naugus stealing some of Eggman's technology. However, the days spent trying to find a base proved futile until Axel the Water Buffalo and his Egg Army chapter arrived; Eggman was able to bluff Axel into taking him to the nearest base. En route, Orbot noted that he had no recollection of Eggman's forces being known as the "Egg Army", nor that Axel was the leader of the Efrika division. The doctor acknowledged this, but quickly dismissed it, being more keen on eating, drinking, and getting back to the Death Egg. At the Efrika Egg Army base, he modified the Egg Mobile into an aircraft and flew off. Prior to departure, however, he checked the EggNet and discovered that strange purple fissures were appearing all over the planet. It was clear to the doctor that something was amiss–and he knew it was his fault.

Eggman's next stop was Avalon, where he was attacked by a G.U.N. aircraft. Confronting Lord Hood, he demanded to know what was going on before modifying his Egg Mobile into an Egg Walker. Attacking a G.U.N. aircraft carrier, Eggman ravaged it before commandeering a G.U.N. fighter jet and escaping. Next, he arrived in Artika, where Tundra the Walrus had prepared a craft to get him back to to the Death Egg During the journey, Orbot and Cubot became worried of Eggman's haste at getting used to his new surroundings, but Eggman was more concerned about the purple cracks forming in the planet's surface. Before long, the trio finally made it back to Death Egg. Taking his seat on the bridge, Eggman asked his lackeys for a report, expecting good news. To his annoyance, however, he got bad news instead; in the new reality, the Knothole Freedom Fighters had never been decimated as before, and had been busy undermining his plans as usual, most recently in the Metropolis Zone. Demanding more reports, the doctor learned that Sally Acorn had been aboard the Death Egg during his absence and fled just hours earlier. Eggman, hoping to kill the princess before Sonic could see her again, dispatched Metal Sonic to pursue her; however, the attempt ended in failure.

As the Death Egg was preparing for takeoff, Eggman finally revealed what he had discovered in Efrika: the power of the Super Genesis Wave had been too much for the fabric of reality to withstand. The entire multiverse had collapsed upon itself and promptly rebuilt itself as something completely different---their molecular structure had even been altered to accustom to the changes. Even worse, all of the residual Chaos energy left over from the Super Genesis Wave's collapse had been trapped within the world and was now trying to escape---a process that was going to destroy the entire planet. By then, the apocalypse was already too late to prevent: at that very moment, the surface of the world shattered into dozens of pieces---and Eggman, for all his genius, ultimately had no idea about how to rectify it.

The Shattered World
Sometime after the beginning of the crisis, Eggman, Orbot and Cubot surveyed the damage to the planet from the Eggnet satellite data. Eggman claimed that all of the damage was the darkest consequence of the Super Genesis Wave's energy shadow and that the reality damage had been done beyond repair. Angry over having to conquer a broken world, Eggman quickly searched his Eggnet for anything in regards to the planet's breaking apart that he could potentially use to overcome this crisis. He then found an article about Professor Pickle's research on the Gaia Manuscripts and asked his henchbots if there were any Egg Army units near Spagonia. The bots give him a negative, due to them being busy securing their territories following the disaster and their transmissions being jammed in the process. He then asked if any Badnik Hordes are near, and Orbot revealed that E-106 Eta's unit was the nearest. Eggman then ordered them to send Eta and his squad to Spagonia University to grab anything and anyone related to Pickle's research there.

Eggman was waiting at Rail Canyon Zone Station for the Egg Train carrying his captives and their research, only for it to arrive badly battered. Despite Orbot's positive note that the train arrived on time, Eggman shouted an order to give an inventory of what was lost. As Eggman opened boxes containing the research in the cart where the Professors where held, Orbot gives the final inventory report: while fuel and munitions remained intact, there was also a total loss of the Badnik Horde, all food spoiled, his two captives gone, and his customized foosball table destroyed. Unbeknownst to either of them, Cubot's mop, of which he was using to clean up the dark energy that broke from the Freedom fighter's battle, had come to life and begun chasing him. Orbot noted that Eggman didn't throw a tantrum despite the losses, but the doctor felt that he had obtained "what really matters" in the form of the Gaia Manuscripts.

Promptly, Eggman called Axel to give a strict order to protect his base at all cost, suspecting it to be one of the Gaia Temples. Later, he hired the Hooligans to search for Chaos Emeralds while he was busy with the crisis. After the trio of mercenaries lost a Chaos Emerald to the Chaotix and Knuckles the Echidna, Eggman ordered them to make amends by entering the Chaos Emerald Championship in Casino Park. Later, Egg-Bosses Cassia and Clove contacted Eggman to inform him that a Chaos Emerald they had discovered in Crystal Cave had been stolen by the Knothole Freedom Fighters. Realizing that Sally must have obtained the information on the cave from the files she stole from the Death Egg, Eggman contacted Thunderbolt, another of his Egg-Bosses. To his surprise, she had been about to contact him with news of a newly discovered Chaos Emerald. He then ordered her to hang onto it, reasoning that the Freedom Fighters would soon arrive in search of it, allowing her to lure them into a trap. However, he first made an attack on the Sky Patrol, the Freedom Fighters' mobile base, using his new War Walrus. When Rotor Walrus thwarted his intentions, he decided upon a new strategy using a brand new Tails Doll. As expected, the Freedom Fighters came looking for Thunderbolt's Emerald, and succeeded in capturing it despite Thunderbolt's trap due to Sonic's unexpected transformation into the Werehog. A very angry Eggman ordered her to ensure that another Emerald didn't fall into their hands, and began debating over the virtues of Roboticized slaves as opposed to Cyberized minions. However, he was then informed by Orbot that the chaos caused by the planet breaking apart had actually allowed the Egg Army to gain ground while their opponents were stretched thin. After learning as well of the massive amount of Dark Gaia energy around the planet, Eggman decided to keep the Chaos Emeralds and Gaia Temples secure to prevent the planet's restoration. He then began making plans to build a facility to concentrate and refine the Dark Gaia energy. When the Freedom Fighters made an attempt for the second Emerald located in Soumerca, Eggman had E-100 Series units Lambda, Kappa, and Iota in position to intercept them, which Orbot considered overkill. The Freedom Fighters barely managed to escape, but Eggman successfully secured the Emerald and inserted the Tails Doll aboard the Sky Patrol while the defenses were down.

The next Emerald was in the possession of Eggman's former minion Breezie, who had organized the Chaos Emerald Championship to decide who would claim the gem. Eggman contacted her and demanded that she turn over the Emerald to him. Breezie refused to do so, however, countering Eggman's threats of attack with the reminder of the strain put on his resources by the planetary crisis. She then reminded him that he would be fighting his own robots if he did attack her, and then noted that he would lose his best export if he cut off her supply. An offer to buy the Emerald off of her was rejected, as she noted that her tournament was a huge hit with Mobius' populace and a boon to her entire network. Much to Eggman's irritation, Breezie put him on hold while she checked on another matter, and then hung up on him in the midst of his tirade. Furious at her defiance, he contacted the Hooligans and ordered them to sabotage Casino Park's defenses in the event that they were unable to win the tournament, only to receive another irritation as Nack insisted upon being paid for any sabotage. Eggman begrudgingly agreed, but warned the Hooligans not to fail him again. He then contacted Metal Sonic, who at the time was on a mission in Apotos, and sent him to Casino Park as well. As it turned out, Sonic, Tails, and Amy were also competing in Breezie's tournament, as were Knuckles, Espio, and Honey the Cat. The Hooligans decided to play by Breezie's rules at first, but were eliminated one by one; by the final round, only Sonic and Knuckles were left. Undaunted, Eggman gave the Hooligans clearance to proceed with the backup plan in preparation for Metal Sonic's imminent arrival, determined to put Breezie in her place despite acknowledging how far she had come in her own endeavors.

Eggman watched the final match between Sonic and Knuckles, but to his frustration Metal Sonic's attempt to claim the Chaos Emerald was thwarted. The doctor thus set his sights on Gregorios, a sage from Apotos with information about the Gaia Temples. An early foray led to an encounter with Sonic, who engaged his Egg SWATs. However, the battle was interrupted by the attacking Ifrit, who emerged from a strange interdimensional gateway. Eggman fled the scene as his robots were destroyed, but kept one in the area that monitored Sonic and his subsequent discussion with Silver. Eggman began pondering how he could turn the portals to his advantage, and set his sites on a new target: the Lost Hex. He set about establishing a base there while Metal Sonic went after the last unclaimed Chaos Emerald, only for his robot enforcer to end up trapped in another dimension. Frustrated, Eggman turned his attention to his other schemes, unaware that he was about to be usurped.

Worlds Unite
Eggman's domination of the Lost Hex's resident villains, the Deadly Six, was brought to a crashing halt when Orbot inexplicably smashed the Cacophonic Conch that forced them to serve him. It was only the first of many unpleasant developments for Eggman, as Orbot proved to be the host of a computer virus from the future of Dr. Wily's world. This artificial intelligence forced Eggman to build him a new body and was thus reborn as Sigma-1, who informed Eggman that he had further plans that required Eggman's technical skills. Recognizing that Eggman needed help, he added one more unpleasant twist: he opened a Genesis Portal and brought Eggman's old ally turned enemy Dr. Wily to be his new assistant. The pair were forced to convert Eggman's facilities into a Mechaniloid factory, and to begin work on Sigma's Unity Engines. However, Eggman began seeing how they could turn Sigma's megalomania to their advantage, and the pair began laying plans to gain revenge on their captor and their heroic foes. At their suggestion, the now armored and mind-controlled Deadly Six were dispatched to capture Sonic and Mega Man.

With the blue heroes in their grasp, Eggman and Wily continued discussing their schemes, during which Eggman learned that Wily had no memories of their previous alliance. He thus spun a web of lies to restore their former positive relationship, while also revealing how they had ended up working together in the altered reality. They then transformed their adversaries into the newest Roboticized Masters, Sonic Man and M'egga Man, and sent each corrupted hero to attack the other's world. While they claimed to be carrying out Sigma's orders, secretly they planned to have the two weaponized robots restore each other to normal and then join forces against Sigma. The two enslaved heroes soon accomplished their task, but as Sigma's power grew Wily became concerned that they had done their job a little too well. Eggman assured his partner that everything would work out, as their subterfuge instantly took effect. However, realizing that Sigma would recognize their treachery, the pair fled, and were soon pursued by the Deadly Six.

Lamenting that their plan to have Sonic and Mega Man returned to normal hadn't been fulfilled on the Lost Hex, the two doctors were unexpectedly rescued by Xander Payne, who offered them his help despite Wily's firm conviction that he wanted to see Wily dead. The trio emerged from one of Xander's Genesis Portals onto the bridge of the Sky Patrol, where they were promptly imprisoned by their nemeses. The pair then admitted to turning Sonic and Mega Man into Sigma's pawns, but claimed it had been Sigma's idea and offered to help stop him in exchange for being released from the brig. They then set to work helping the heroes prepare for the coming battle, examining the Power Ring engines of the Sky Patrol. Eggman had to admit a certain jealousy as they watched Tails examine Wily's Robot Masters, but he and Wily soon set to work on a new project. They were urged to hurry as the heroes engaged Sigma's Mechaniloids and the Deadly Six, and successfully accomplished the task after the Zeti had taken control of the robotic heroes. Their Egg-Wily Uppity Robot Scrambler Cannon freed the Zeti from Sigma's control and the heroes from theirs, and the aliens were then thrown into the brig. Unfortunately, Sigma chose that moment to unveil his massive new robot body and the army of Mavericks he had Time-Cloned to serve him.

Sigma ended up sending most of his forces to various worlds to set up more Unity Engines, and the handful who remained were dispatched by the arriving heroes of the Street Fighter Zone. Sally then proposed that they split up to stop the Mavericks and try to recruit other heroes to join their cause. Eggman suggested that they also form a backup plan, and volunteered to have Metal Sonic recover his single Chaos Emerald to join the six already aboard ship. In reality, however, Eggman and Wily planned to reach the Master Engine and secure its power for themselves, and were assisted in this endeavor by Xander.

Trying to Conquer One World
Upon reassuming command of his empire, Eggman would set out to recover his lost enforcer, Metal Sonic. Using his Big Arm vehicle, he entered the Distant Abyss Zone where Metal Sonic's coordinates were found to be. He was attacked by a mysterious creature there, but Metal Sonic winded up using the last of its power to save the doctor, who successfully fled the zone with his robot.

Later, the Naugus Twins soon seized control of Eggmanland and captured Metal Sonic. Eggman decided to retaliate by summoning all eleven of his Egg Bosses to retake his refinery. Due to having an odd number of Egg Bosses, Eggman teamed up with Axel. Soon, a Dark Gaia Titan nearly killed Eggman but was rescued by Axel. After the other ten Egg Bosses completed their missions, Eggman confronted the Naugus Twins and Crystal Sonic- Metal brainwashed by the twins. Using his Hard-Light Armor, Eggman defeated Walter and returned Metal to his senses. Eggman then made Wendy an Egg Boss, due to wanting an even number of Egg Bosses, as well as having an Egg Boss with magic powers.

Eggman soon tracked down Phage, and began to berate her for her failures. Eggman then watched Sonic and Sally's worldwide broadcast (transmitted by Tails Doll). This revealed to Eggman that the Freedom Fighters have regained the seven Chaos Emeralds, and Eggman also learned about Gaia Keys for the first time. Eggman immediately decided to plan and assault, telling Egg Boss Battle Kukku XV to take down the Sky Patrol, Nack to rob Castle Acorn to steal the Chaos Emeralds, Wendy to send her minions, the Witchcarters, to aid the Hooligans, and Phage to link with Tails Doll.

Eggman had his minions kidnap Gregorios and forced him to reveal the location of the Gaia Gate. After he received the Chaos Emeralds, Gaia Keys, and Chip, Eggman requested Speedy and the Battle Bird Armada to take down a nearby G.U.N. flying carrier. Eggman then forced Chip to activate the Gaia Gate and had his Egg SWATs place one emerald in one Gaia Temple. This caused the temples to rise up out of their respective locations and assemble in Apotos to form the Gaia Colossus.

Soon, Eggman went to Eggmanland and was informed that the Freedom Fighters had infiltrated. This prompted him to activate his new Egg Dragoon mech to finish off Sonic once and for all. The two engaged in an intense fight and the evil scientist tried his best to prevent Sonic from reaching the Gaia Colossus' head, where Chip was. Eggman was eventually able to freeze Sonic in place and attempted to impale him but unfortunately for him, Sonic had transformed into the werehog and stopped his attack. Sonic was able to overpower Eggman and the mad doctor was thrown out into the open with his Egg Mobile. Eggman ordered Orbot to power up the Death Egg at the Summoning Spire immediately but Orbot could not as Eggman Land was submitting very dangerous readings.Defeated, Eggman watched Super Sonic and Chip battle Perfect Dark Gaia while he lamented the loss of Eggman Land. He then began to hatch a plan that involved siphoning the raw power of the world to power up his Death Egg. Later on, Chip was able to restore the world and the irritated Eggman received a pat on the head from Cubot.

Appearance
During his service to the Kingdom of Acorn, Eggman had a round torso and 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, and mirrored pince-nez sunglasses.

In the present day, Eggman remained obese but has become somewhat burlier, taller and less flabby with long, almost disproportionately thin arms and legs. He now wears both tinted glasses and goggles as headwear, through his moustache retains its length, density and mass. Gone are the cape and his suit-like clothes, in their 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.