Sonic lands in Mushroom Hill and resolves to destroy the Death Egg before Dr. Eggman repairs and re-launches it. He soon notices Knuckles the Echidna, the guardian of Angel Island who has been tricked into helping Eggman. Sonic would ultimately have a showdown with Knuckles in the Hidden Palace. However, the two see Eggman stealing the Master Emerald. Knuckles makes amends with Sonic, whom he guides to the Sky Sanctuary. There, the hedgehog encounters Mecha Sonic Mark II, a powerful robot resembling himself, but manages to board the Death Egg. After Sonic's story, Mecha Sonic Mark II plots an attack on Angel Island, enlisting an Eggrobo as his subordinate. This Eggrobo ambushes Knuckles but Knuckles survives! Knuckles eventually arrives at the Sky Sanctuary, where he discovers that Mecha Sonic has stolen the Master Emerald, causing Angel Island to slowly fall from the sky again. Now both Sonic and Knuckles need your help!

Sonic: Eggman really did it this time.

Knuckles: No kidding. Mecha Sonic is powerful.