When Eggman seemingly killed Sonic by trapping him in a capsuled rigged to explode, Tails took up Sonic's mission to save the world himself and promised to avenge his friend's death by defeating Eggman.
The first battle takes place in an area of Weapons Bed. The player must focus on the Volkan Cannon over the Lock-On Missile to attack Eggman, as the missiles are too slow to catch him. When Eggman is near Tails, it is recommended to use the Propeller Punch fast or he will retaliate.
During the battle, Eggman will attack by using his Volkan Cannon when he faces Tails, and his Lock-On Missiles when Tails is far away. Meanwhile, Eggman will move around to avoid the player's shots, before closing in to attack. It is thus best to attack Eggman when he is heading straight for Tails. When within range, Eggman will also use Punch. The player has to hit Eggman four times to win.
The second fight takes place in the central control room on the Space Colony ARK. This battle is harder than the previous one. Eggman is now faster and smarter than before, and is armed with two new attacks. The Power Laser can land two hits at once if Tails is nailed directly, and the Rocket Launcher sends out a shower of homing missiles that can cause big damage if they make contact.
To defeat Eggman, the player again has to focus on using the Volkan Cannon for faster hits. Alternatively, the player can use the Lock-On Missile to detonate a Dynamite pack in the middle of the room at the right time, thereby triggering a wide explosion that can damage Eggman should he get within range. After losing half his health, Eggman will start using his special attacks. The missiles can be avoided by running and the laser can be dodged by getting close and moving to the sides. The latter attack especially leaves Eggman vulnerable, making it possible to attack him and make him turn off the Power Laser. Five hits are required to defeat him.
The fight against Eggman in the Hero story is identical to the fight against Tails in the Dark story.
Eggman is the only boss in the game that Tails fights.
Eggman does have all his Level Up Items for the second battle, unlike Tails in the Dark Story.