After the player has completed all the Attractions in the game, Metal Sonic will appear in the Stage Select room and port himself into the stage select machine. The player then has to hit the bumper as they would when they select an attraction to select one of the four numbered panels or the X. Metal Sonic will perform a different attack based on what number is selected:
- Two platforms on the far left and far right raise up into spiked walls. Two fin-like objects then raise from the floor and move outwards towards the spiked walls, causing the player damage, before moving back to the center.
- A long tentacle emerges from one of the flashing lights on the machine and bounces on the floor in an effort to attack the player. After that, the light on the other side of the screen repeats the process.
- A number of rockets fire up from the ground, falling back down and exploding, damaging the player.
- Two saw-blades come out of the ground and move across the screen, attempting to damage the player.
Selecting the X destroys one of the numbered panels, removing that attack from Metal Sonic Kai's arsenal. Once all panels are destroyed, Metal Sonic will be defeated and flee. A small cutscene plays and afterwards, the player has to face the final boss.
- In the Japanese manual, Metal Sonic was given the name Metal Sonic Kai (メタルソニック改?). This alternate name is explained as Metal Sonic's original body being damaged beyond repair after his last encounter with Sonic. Dr. Eggman transferred his CPU over to a replacement body he made with Dark Ring energy, also giving him a new component that enables the Plasma Pulse Attack. Contrary to popular belief, it does not apply to the final boss creature.
- In Japanese, the Kanji of "Kai" used in this case (改) translates to "revised" or modified." His name literally means "Revised Metal Sonic" in English.