* For the first boss fight in Episode 2, [[VideoGame/SonicTheHedgehog2 the stone columns from Aquatic Ruin Zone]] rise from the ground. [[spoiler: Then Eggman reveals a giant plant-machine, and smashes the columns, indicating he's finally getting serious and not using boss rehashes!]]
* Eggman's second boss in Oil Desert Zone. His Egg-O-Matic sprouts a large electromagnet and assembles a giant robot made of scrap metal in ''seconds''.
* The fight against Metal Sonic on the roller-coaster ranks as one of the most intense Sonic boss battles ever, where Metal shows up still smarting after losing to you in ''VideoGame/SonicCD'' and is determined to make you hurt. And ''goddamn'' if he doesn't throw everything at you to do so.