The Babylon Rogues rush to the former site of Castle Acorn, now a deep crater. As they descend, betraying the Battle Bird Armada, Sonic is approaching at high speed, having broken free of the anti-gravity bubble he had been briefly trapped in. He attacks the Rogues in mid-fall, only to be trapped in the bubble again once they hit the bottom. The Rogues continue on, knowing Sonic will be free soon. They find the city and its control center. As Jet combines the cube-like key and the ring, the cube flies out of his hands and into a slot. A robot connected to the controls comes to life, the city now being powered by the cube.
The robot answers some of the Rogues' questions, revealing that the Babylonians are actually aliens, and the Babylon Garden was a way to transfer Chaos Emeralds and other powerful gems across the universe. He also says that Eggman's A.I. "son" A.D.A.M. actually detected and wanted to tap into the power of the Gardens, one of the reasons the original nanites were released. The Garden itself is a spaceship. Sonic bursts into the room, hurting the Rogues. The robot then begins to pilot the ship and initiate its teleportation cycle to return to the homeworld and be repaired. However, doing so will result in a black hole that will destroy the planet. Jet tries to stop it, but doesn't have the proper clearance. Outside, the Battle Bird Armada attempts to grapple onto the Gardens and hold on so that it doesn't escape their grasp, and the Battle Lord sends Speedy to stop the Rogues, though he is easily stopped.
Sonic takes and destroys the cube/key/energy matrix, sending the Gardens and the Armada's ship crashing into some mountains. Sonic escapes through a door, regretting that he was a good guy and couldn't morally teach the Rogues a more prominent lesson. He rushes to the outskirts of New Mobotropolis and talks with Rotor Walrus. Rotor is controlling the nanites manually to rebuild the city, though without Nicole it will take significantly longer. In the mountains, the Babylon Rogues recover and escape before the Armada can capture them. Jet says that now he has the goal of becoming the fastest thing in the universe.
Jet, Wave and Storm are seen on their Extreme Gears. Jet is happy to see that the trio have finally found the Babylon Garden. However, they have really found an ordinary garden with a farmer growing butter beans. The trio are speechless.