After Eggman and Infinite were defeated by the Resistance in the epic war between the Resistance and the Eggman Empire, Eggman was in limbo, and escaped, having amnesia. He had no memory of his attempts to conquer the world, so he started a new life as a scientist for the United Federation. The Resistance and GUN merged together, creating a new alliance with new shared technologies and friendships, only to have Knuckles's role as Resistance leader overtaken by Abraham Tower, the GUN Commander.

Infinite had returned, overtaking Eggman's old empire, and renaming it the Infinite Empire, bearing a red flag with his mask on it. The war between the Infinite Empire and the GUN Resistance begins...