A number of strange occurrences throughout Mobius in the months that followed lead the Freedom Fighters to investigate satellites circling about Mobius. There they made a horrifying discovery. Dr. Robotnik lived on in the form of a sinister Robotnik from an alternate dimension called Robo-Robotnik. (Sonic 75) This new Robotnik took on a persona called Dr. Eggman and continued Jullian Robotnik's work in the form of the Eggman Empire.
Before the war with the new Empire could reach a fever pitch a new threat presented itself in the form of a destructive alien race called the Xorda. (Sonic 125) The Xorda came to a planet called Earth 3,000 years ago only to be attacked by the native humans when they tried to form an alliance. They retaliated by releasing Gene Bombs in an attempt to wipe out all life on the planet. Having discovered that life still exists on the redubbed planet Mobius they returned to the planet that wronged them in hopes of exterminating life there again. A Freedom Fighter named Sonic the Hedgehog selfishly sacrificed his life to ensure that the weapon used against Mobius caused an isolated explosion instead of a black hole creating implosion. The act surely killed Sonic ...
... or so it seemed.
Sonic the Hedgehog returned to Mobius after nearly a year's absence to find the mobians fighting an all out war against the Eggman Empire. While the Kingdom of Knothole flourished in The Great Forest the Eggman Empire tightened its grip on other parts of the world and forced smaller communities to converge into Knothole (for mobians) and Station Square (for Overlanders). The great city of Echindaopolis, once a powerful ally to Knothole, never fully recovered from constant attacks by enemy forces from all corners leaving the echinda population ravaged and desperate for help. A small group of echindas eventually situated in their homeland; Albion.
On the eve of what appeared to be a time of great happiness for the Freedom Fighters Eggman attacked at full force in a move that destroyed Knothole and nearly destroyed everything that the mobians held dear. (Sonic 175) A small group of rebels lead by NICOLE launched a successful attack that put the war back in the mobians favor. To show her gratitude towards her friends NICOLE founded the city of New Mobotropolis for the newly rescued mobians to live in. Here the mobians started breaking down the defenses of Eggman's crumbling empire in preparation of launching a final assault against the tyrant.
In the middle of a critical assault against the Eggdome Freedom HQ was attacked by a group of invaders from Moebius. Rather then heed the ruling of the Acorn Council to continue their assault on Eggman the Freedom Fighters launched an counter invasion on Moebius to find a way to drive back the moebians. (Sonic 189 - 196) The battle against King Scourge was nearly lost when he gained access to his long dormant super form but a clever ploy by Sonic caused the King's downfall. Scourge, a frequent zone hopper and troublemaker, was captured and imprisoned in No Zone since he was no longer welcome even on his home planet. Sonic returned to Mobius after one last strenuous battle with his counterpart to begin planning the final attack against Dr. Eggman.
The Storyline begins a few days before the events leading up to the fall of the Eggman Empire in Sonic 198.