Dr. Eggman: The egg-shaped, mustached antagonist of the series. Eggman has a passion for building robots and weapons which he attempts to use to conquer the world. In this game, he has built the Egg Fleet, a giant army of battleships that resemble fish. However, Eggman is not the main villain in the game and has fallen to the wrath of one of his own creations.
Metal Sonic: Metal Sonic is the robotic counterpart of Sonic, built by Dr. Eggman. Metal Sonic has betrayed Eggman in this video game, taking the destruction of Sonic into his own hands. He has obtained a data-copying ability as well as an emperor-like design. In the Final Story, Metal Sonic transforms into a giant metal dragon called the Metal Overlord.
EggPawn: Grunt Soldiers of the Eggman Army, and the ones you will encounter the most often. These guys bear the most resemblance to Eggman himself, and carry all manner of weaponry: Automatic Rifles, Rocket Launchers, Shields, Lances, and more.
Flapper: Similar to EggPawns, you will encounter Flappers extremely often. Generally, they hover in one place, stationary, although some fly around with search lights in order to call in re-enforcements upon spotting you.
Rhino Liner: Found only in the Rail Canyon/Bullet Station stages, Rhino Liners travel along grind rails in an effort to knock you off.
Falco: Smaller versions of the Egg Hawk boss. Usually only found in the Egg Fleet stage.
Klagen: Giant purple and blue squid-like robots. If a Klagen catches a teammate in it's capture beam, that teammate will be unusable until the Klagen is defeated.
Cameron: Turtle robots. Generally can only be defeated by flipping them over on their backs and striking their stomachs. Have giant cannons mounted on their backs.