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The Invasion of the Eggdome was the final push to try and overthrow the Eggman Empire by the Republic of Acorn. To accomplish this, they sent in two strike teams: The Knothole Freedom Fighters and the Chaotix. The two groups secured themselves a campsite outside of the Eggdome to ready for the invasion the next morning, and then held a brief battle inside with the Echidna Dark Egg Legion. Once they'd regrouped, the two teams discovered a barricade that only Sonic the Hedgehog could fit through. He zoomed through it using a spin-dash and fought Dr. Eggman in his Egg Tarantula. Sonic won, and the numerous defeats finally caused Eggman to snap and he went insane. Without Eggman to stand in their way, the Iron Dominion then took over the Eggman Empire.
Soon after the wedding of Antoine and Bunnie D'Coolette, Eggman launched his new Egg Fleet and two Egg Beaters. Snively, in his Egg Beater, invaded Freedom HQ and teleported as many of the Freedom Fighters and Chaotix as he could to the Egg Grape Chambers before having his Egg Beater self-destruct, leaving only Sonic, Tails, Knuckles, Amy Rose and NICOLE behind. Sonic zoomed off to Knothole to find most of it destroyed except for Castle Acorn, which Eggman himself emerged from it in his Egg Beater, ready to fight Sonic. He proved more than a match for Sonic, and the hedgehog returned to the ruined Freedom HQ to tell his friends Knothole was gone. Luckily, NICOLE had a plan at her disposal. She had been constructing a city of nanites from the remains of A.D.A.M.'s city she'd christened New Mobotropolis and thought that if they freed everyone and reset the teleporting technology in the Egg Beater, all they'd have to do was let Eggman re-capture his prisoners so they'd be sent to New Mobotropolis where they'd be safe from the Egg Beater and the Egg Fleet because of its force field. After the plan was successfully put into action, the Freedom Fighters and Chaotix fought the Egg Beater again, this time tearing it apart so Eggman had to fly home on one of his robots. (StH: #174, #175, #176, #177)
After Knuckles the Echidna was brainwashed into becoming Enerjak by Doctor Finitevus, he destroyed most of the city of New Megaopolis, leaving only the Eggdome operational. With no robot troops to back him, Eggman made a deal with the Dark Legion to restore their cybernetics for their services, implanting bombs along with them to ensure their loyalty. (StH: #180, #181, #182, #183, #184)
For a while, Eggman was at the mercy of the Knothole Freedom Fighters and their allies, the Chaotix, even managing to blow up a communications tower that prevented Eggman from contacting half of the planet. He tried to fight back by sending in the new Metal Sonic and Metal Scourge robots, but they were defeated by the combined effort of the Suppression Squad and Sonic. (StH: #189, #190, #191, #192)
Eggman then retreated to his lab, his mind gradually slipping, continuing to create deadly machines such as the Egg Phoenix and Egg Tarantula, and converting a telescope into a super laser that would destroy half the Eggdome along with the Freedom Fighters. (StH: #194, #197, SU: #2)
Finally, the Freedom Fighters struck back and secured themselves a campsite protected by a forcefield after the Dark Egg Legion failed to push them back, and Eggman's Egg Phoenix was destroyed. The following night, G.U.N. agents Shadow the Hedgehog and Rouge the Bat teamed up with Sonic to destroy the Doom Laser before heading back to G.U.N. HQ. The next day, Eggman launched E-123 Omega to destroy E-102 Gamma in order to ensure his final showdown with Sonic went as planned without interference from traitorous robots. The Dark Egg Legion then readied themselves for the battle as the invasion began. (StH: #198, SU: #2, #3)
Eggdome InvasionAfter they had set up a link to New Mobotropolis, the Chaotix and Freedom Fighters started their assault. At the same time, Lien-Da ordered the Legion to begin their defense and work on the barricade. Mighty and Bunnie then broke open the front door and the Freedom Fighters took to the West hall while the Chaotix took to the East hall. After both teams defeated the Legion, they met up at the barricade. After a brief conversation, Sonic spin-dashed to meet Dr. Eggman in his Egg Tarantula. After a brutal fight against his nemesis Sonic once more defeated him and destroyed his machine, declaring victory, at that point Eggman lost his last hold on sanity and the heroes went home happy that the tyrant was defeated, though Sonic felt shaken by what had happened to the Doctor. (StH: #199, #200)
After Eggman had lost his sanity and the Freedom Fighters went home to celebrate, Snively placed him in a padded cell and then welcomed the Iron Queen, the Iron King, the Bride of Conquering Storm and the Yagyu Clan on top of the Eggdome with the Echidna Dark Egg Legion. Shortly afterward, Eggman regained sanity and returned to the Eggdome with the Dark Egg Legion in a new attempt for total conquest. (StH: #200, #211, #212)