Having parted with Sonic and the others, Knuckles, who is taking independent action, hides in the city. There, he comes in contact with Eggman, who claims that he wants to collect the Chaos Emeralds to return to their own world and apologizes for the evil deeds he has done until now, asking Knuckles to deal with Sonic. Knuckles is tricked by those words. It is then reported that an unidentified gem has been discovered. It turns out to be a trap Eggman had made up, but Knuckles and Sonic's group fall for it. That's where Sonic and Knuckles begin their fight.