On Angel Island, Eggman confronts Knuckles who demands the latter to hand over his Chaos Emerald. Sonic soons appears and Knuckles (turning his attention to Sonic) isn't all thrilled to see him. However, Eggman takes advantage of the distraction and takes the last Chaos Emerald gloating on his success of doing so. Sonic askes Eggman what he is going to do with all of the Emeralds and Eggman replies that he would take over the world. He also plans to put together his greatest invention yet: the Brainwash Beam. Eggman escapes and Knuckles blames Sonic for the loss of the Emerald. Sonic askes Tails where Eggman may go next and Tails, knowing Eggman has to transmit the beam over the entire world, concludes that Eggman may head for outer space. Tails says that Eggman may have a rocket in South America to launch into space and Sonic prepares to chase after him.
The Zone consists of three acts followed by a boss fight against Dr. Eggman at the end of the third act. If the player reaches the goal with at least 50 Rings, they will receive a fragment of the green Chaos Emerald.
During this boss fight, Dr. Eggman is in a mech that now has two spiked balls spinning around that have greater range. Sonic must fight Eggman in an area where platforms at the bottom explode on contact causing Sonic to jump upwards. Sonic must carefully time the jumps and hit Eggman three times when the spiked balls aren't around to defeat the doctor.