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Arriving with Tails at the Floating Island in the Tornado, Sonic uses the seven Chaos Emeralds he had acquired prior to turn into Super Sonic and begins exploring the island while Tails tries to follow. Shortly after arriving on the island however, Knuckles pulls off a cheap shot on Sonic from below, causing him to lose his Super State and drop the Chaos Emeralds. Knuckles proceeds to take the Chaos Emeralds before running off.^[9] Now having to retrieve the Emeralds again and stop Dr. Robotnik, Sonic and Tails make their way across the island, dealing with Robotnik and Knuckles' attacks along the way. Eventually, they arrive at Launch Base Zone, Dr. Robotnik's base where he has almost finished re-building the Death Egg. At the end of this Zone, the Death Egg is ready to take off. To reach the Death Egg, Sonic and Tails hitch a ride on a nearby Egg Mobile, though Knuckles keeps them from proceeding with it. Fortunately, local tremors causes him to lose his balance and fall down from the pillar he is on, allowing Sonic and Tails free passage. In the end, the duo manages to jump onto a platform on the Death Egg just as it starts to take off. There, Robotnik returns to defeat Sonic through excessive force with the Egg Rocket. As Sonic and Tails defeat Robotnik once more, the battle has already taken its toll on the Death Egg during a critical point of its launch, and the space fortress plummets back to the Floating Island while Sonic and Tails watch from afar.^[9]

Immediately after, Sonic and Tails fall to Mushroom Hill Zone. Meanwhile, the Death Egg lands in the Floating Island's volcano, still intact enough for Dr. Robotnik to salvage it and re-launch it. Aware of this, Sonic and Tails continue their mission to destroy the Death Egg. However, their quest is suddenly interrupted when they spot Knuckles appearing from a hidden door in the thicket. After carefully examining the vicinity, Knuckles disappears into the forest. Once sure that Knuckles is gone, Sonic and Tails emerge from their hiding place and open the door from where Knuckles came out of with a nearby Switch. Inside the hidden room, they are caught in an overflowing, dazzling light. Taking a closer look inside the light, they see a Super Ring. Unable to quell their curiosity about what this ring could be, they touch it, causing them to be taken to Hidden Palace Zone, a giant solemn hall with a pristine altar. There, they see some pillars with the Master Emerald and some other stones, which use the power of their Chaos Emeralds to become inert Super Emeralds. Filled with questions, Sonic and Tails decide to set off to power the Super Emeralds, stop Dr. Robotnik from re-launching the Death Egg again, and discover the mystery of Hidden Palace Zone.^[10]

Sonic watches the Death Egg take off from Sky Sanctuary Zone.

Making their way though the Floating Island, Sonic and Tails arrive in Lava Reef Zone, the location of the Death Egg. In an attempt to stop the heroes, the space fortress uses its laser eyes to reactivate the volcano. Surviving this attack, the duo arrives in Hidden Palace Zone again, where they have a battle against Knuckles. After Knuckles is defeated though, he, Sonic and Tails witness Robotnik stealing the Master Emerald with the Egg Mobile. Enraged, Knuckles tries to stop the doctor, only for the latter to electrocute him and escape. Realizing that Robotnik has lied to him and that Sonic and Tails are actually trying to save the Floating Island, Knuckles takes the heroes to Sky Sanctuary Zone, where Sonic and Tails continue onward, dealing with Mecha Sonic Mk. II along the way, before managing to get onboard the Death Egg.

With the Death Egg having made it into space, Sonic and Tails pass though Dr. Robotnik's many contraptions, before fighting Robotnik and his Giant Eggman Robo, a mech powered by the Master Emerald. After losing the battle, Robotnik tries to escape in his Egg Mobile with the Master Emerald, only to be stopped, triggering a chain reaction that causes the Death Egg to crumble and explode. From here, the ending of the game will depend on the player's progress