After Doctor Eggman's success in distracting G.U.N, to give Rouge some time to obtain the three Chaos Emeralds, the doctor ordered Shadow to go rescue Rouge after she ends up imprisoned on Prison Island, with a manual bomb set to destroy the island. On his way to do so, he encountered Sonic again and engaged him in a fierce battle. However, they do not complete it, as Eggman notified Shadow again of the bomb.
Eggman had been defeated at the hands of Tails, and could not move, so he requested Shadow to go and locate the one that escaped to the core of the Eclipse Cannon. After discovering that person was Sonic, they both formally introduced themselves to one another, before beginning their final battle in their respective stories.
In the first battle, the player must look for Sonic's moves. As when he is near, he will do a surprising Homing Attack at the player, so must evade being near. There are two ways to hurt Sonic, one to watch when he is on the ground, and launch a Spin Dash at him at a fast rate, or waiting for him when he stops and sit still. The player must hit him three times to defeat.
In this battle, Sonic is now more fearsome than in the previous battle. The player must now race Sonic along an infinite line of platforms that fall into a bottomless pit one after another behind Sonic.
At the beginning, the player must launch a Homing Attack or Spin Dash at Sonic to hurt him. If the player takes the lead in this race though, Sonic will teleport up in front using Chaos Control or launch a Homing Attack at Shadow to hurt him and take the lead. To avoid the latter, the player simply has to use to Spin Jump. After the player has hit Sonic three times, he will complicate his moves and attacks. The player must now get behind him and wait until he stops to launch his Sonic Wind. Before he can launch it though, move in on him, even after he uses the Sonic Wind, to attack Sonic. His Sonic Wind can be avoided by Somersault. Continue this pattern until Sonic is defeated. Sometimes, even the Light Speed Dash can hurt Sonic should he teleport into a trail of Rings.
The fight against Sonic in the Dark story is identical to the fight against Shadow in the Hero story. However, Sonic's warp time is significantly shorter, but the use of Sonic Wind causes Shadow to suddenly skid to a halt when running.
If ten minutes have gone by in the second battle, then the road ahead will collapse with further sections falling down just as they appear. While Sonic is safe thanks to his Chaos Control, the player will eventually die after hitting the death line.
During the first battle, Big the Cat can be seen below a vent.