Of course, all this is contingent on the idea of Knuckles appearing in Sonic the Hedgehog 2 in the first place.
Right now, that idea is simply a rumor, but it’s certainly one that makes sense.
The post-credits scene to the first movie introduced Sonic’s popular video game sidekick Tails and the game franchise has a host of other anthropomorphic animal characters who could appear, and Knuckles is probably the next most well known after Tails.
At different points in the games and other media Knuckles has been a rival to Sonic as well as an ally, so the next movie could make him the new big bad, but end in a way that the pair could work together if we eventually get a Sonic the Hedgehog 3.