After Sonic the Hedgehog chases Eggman down a pathway on the doomed Death Egg space station, Eggman boards the Great Eggman Robo through a hatch in the back of the robot's head. The pathway begins to crumble as the mecha powers up, and after it stops, the mecha sidesteps across in the background. Three large metal fingers appear behind Sonic (the rest of the arms are not visible, in fact only the robot's head can be seen throughout the battle). With every step, Eggman tries to crush Sonic beneath his robot's fingers. Each finger takes three hits to destroy and they are easy to avoid. Once the fingers have been destroyed, Eggman will change tactics.
With its hands destroyed, the Great Eggman Robo shifts its position and the left side of the deck crumbles away as the robot emerges from beneath it. The mecha will then march after Sonic, who must keep moving to the right. The robot's nose is equipped with a flamethrower and will blast fiery bursts at Sonic. Sonic must avoid the flames and hit the robot's nose, which will cause the mecha's "mouth" to open, revealing a glass sphere which houses the Master Emerald inside it. The lens on the sphere will start charging up energy to fire a huge laser beam. Sonic can attack the laser cannon as it is charging, but must jump up as soon as charging finishes to avoid the sudden laser blast. After firing the laser, the Great Eggman Robo will close its mouth and start with its flame attack again. Sonic must hit the laser cannon a total of eight times to destroy the robot.
After its laser is hit eight times, the Great Eggman Robo will explode and start sinking out of sight. Eggman will then appear in his Egg Mobile, which is carrying the Master Emerald in a crane claw. Eggman will then fly ahead of Sonic and Sonic must give chase. The deck behind Sonic is rapidly falling apart, so great care must be taken to keep up with Eggman and defeat him. The Egg Mobile has no weapons or attacks and will just keep flying ahead of Sonic. Sonic must catch up and hit the craft eight times to defeat it.