Returning from Sonic Heroes is the Egg Emperor. The fight takes place on Eggman's battleship from the stage Final Fortress with Modern Sonic as the player's character. In this fight, there are two phases: the first phase is simply circling the arena. Eggman will fire lance waves at Sonic in two directions, horizontal and vertical. You must dodge them and boost to hit Eggman, while also dodging the constant barrage of missles being fired at you from the center arena.
After a few hits, the fight will shift to phase two. Eggman will retreat to the arena, and Sonic will boost over to the outer part of the arena. From here, you can destroy the various missile launchers that were attacking you before, but this is not your primary objective. Eggman will eventually charge you at your location, and if he misses he will look for you frantically. This is when you strike. After he is hit, he will return to phase one again and the cycle repeats.
On his last hit, he will go to the arena. From the middle he will start swinging multiple sword slashes your way in a last-ditch effort to end Sonic. After dodging these, he will try to charge again, and then you can deliver the final blow to end this boss.