Stranded on the Sky Sanctuary Zone, Sonic and Knuckles the Echidna witness the rise of the Death Egg. On board, Doctor Robotnik is triumphant, as Grimer marvels about how the Master Emerald is keeping the ship afloat. Robotnik finally notices the plight of Sonic and Knuckles, running to find the last bit of the Zone still standing. With nowhere left to go, Knuckles glides off with Sonic on his back. Just to make sure there is no way they can survive, Robotnik unleashes his EggRobo Badniks to deal with them. Surrounded, Sonic leaps off and smashes them, fortunately ending his attack crashing through a window of the Death Egg. Knuckles glides back down to the Floating Island, an idea forming. Sonic wanders the corridors of the Death Egg, completely unsure of how to get to Robotnik. He can't think too long as he is attacked by Spikebonker Badniks, which Sonic thinks Robotnik designed on an "off-day". Back on the Floating Island, Knuckles prepares to use ancient technology not used for eons (thanks to the help of ancient texts). Once activated, the island starts to move towards the Death Egg.
Some time later, Sonic is on the bridge with Robotnik, apparently having been captured. Sonic refutes this, saying he was lost and used the Badniks to help him find Robotnik. With Sonic present, Robotnik commands Grimer to charge the disintegrator array and destroy the Emerald Hill Zone. The countdown ends and Sonic can't stop it. However, before Grimer can fire, the ship is hit by a huge quake. They all look out the window to see the Floating Island firing at them. On Robotnik's order, Grimer turns the weapons on Knuckles, locking both structures in heavy combat. As Robotnik proclaims his victory, Sonic knocks the Master Emerald out of the generator, making the Death Egg lose power. Another quake sends Sonic, the Master Emerald and some Eggrobos crashing out another window and the ship is left at the mercy of the Island's power.
Happy that the Death Egg is being destroyed, Sonic's immediate concern is that he is falling to his death. Despite Sonic battling the Badniks, one grabs the Emerald in an attempt to return it to the Death Egg. Sonic steals another Badnik's gun and destroys the Emerald's captor. As Robotnik prepares to evacuate the ship, he vows terrible revenge on the Emerald Hill Folk. Back outside, Sonic has stolen the jet pack of an Eggrobo and headed back to the Island, finding the Master Emerald safely in the bushes. He is interrupted by a furious Robotnik in one of his battle vehicles. Sonic is having none of it and completely rips the machine apart, before accidentally punching Robotnik off the edge of the island. Robotnik is in luck, the vehicle's weapon's damaged jets being good enough to land him on Mobius safely. Knuckles returns and wants the Master Emerald back, but Sonic needs a favour first...
Three days later, the Emerald Hill Folk desert their homes and head to the Floating Island, which has been lowered into the sea. As part of his deal with Sonic, Knuckles will keep the villagers safe in the island's Mushroom Hill Zone, with the whole island now protected by the power of the Chaos Emeralds, now all present and complete. In a hospital bed, Robotnik is seething from his defeat and vows to be a much more ruthless ruler from now on.
- The story ends the Sonic 3 & Knuckles story arc, one that had been running on and off since Issue 33. The two last Zones of the game featured, minus Doomsday. This Zone wouldn't remotely feature until Issue 97, when it was referenced as the name of a story. This is probably completely unrelated, however.
- At the beginning of Part 3, Knuckles is labelled as "Knuckle's".