The first battle takes place in a square field on Prison Island, after Sonic clears Metal Harbor. Shadow will simply attack by jumping and performing the Homing Attack. Sonic has to hit him from behind when he is not jumping to hurt him. Three hits are required to defeat him.
The second battle takes place on an infinite straight track on the Space Colony ARK, after Sonic clears Final Rush. Here, Shadow is the final boss of the Hero story. Unlike before, Sonic must keep running to stay ahead of the falling platforms behind him. There are also meteors that will hurt Sonic when they explode. Like the previous battle, Shadow will mainly attack with the Homing Attack. His other actions depend on his position during the fight. If he falls behind or off the track, then he will use Chaos Control to warp in front of Sonic. If he gets too far ahead of Sonic, he will use his super move, the Chaos Spear. Five hits are necessary to defeat Shadow.
- The second battle against Shadow is remade in Sonic Generations, in one of the three rival battles.
- The fight against Shadow in the Hero story is identical to the fight against Sonic in the Dark story.
- If noticed during the first battle, Big the Cat can be seen below a vent.
- If 10 minutes has elapsed in the second battle, then the road ahead will collapse with further sections falling down just as they appear. While Shadow is safe thanks to his Chaos Control, the player will eventually die after hitting the death line.