After parting ways with Sonic and the others, Knuckles had been laying low in the city.
Then Dr. Eggman approached him and pleaded, “I intend to gather the Chaos Emeralds to bring us home and live in peace. I’ll make amends for my past misdeeds, so please defeat Sonic.” Knuckles was taken in by his words.

Just then, news broke of the discovery of a mysterious gem.
Although it was actually a trap set by Eggman, Knuckles and Sonic’s team headed there anyway.
That’s where the showdown between Sonic and Knuckles began.
However, because the battle dragged on without a clear winner, Eggman, growing impatient, went on a rampage with one of his robots.