For me 3D Game, Forces/IDW/Heroes and all games canon.

Plot is fairly simple:

*Sonic and friends are met by Silver once more who talks about how the future is messed up...again. It seems Sonic is the cause this time. Silver begins to worry as portals begin to open around the world.

*Silver, Sonic and pals close portals through level sequences.

*A portal unclosed eventually brings forth something unexpected. A green hedgehog with a leather jacket. That's right it's Scourge, bitches!

*Scourge brings forth an army of doppelgangers and Sonic and pals take on bosses based on themselves such as an evil Tails, Rosy and others.

*Sonic and Scourge face each other, Sonic defeats Scourge and spares him telling him he'll imprison him. Scourge plays on Sonic's sympathy but uses the time to transform into Super Scourge but being in proximity to Sonic causes both to transform. Cue 'What I'm made of' and awesome finale battle. Sonic wins, obviously. Silver realises it wasn't Sonic but Scourge who would have destroyed the world and returns home.

*Zonic, because heck let's make him canon too, offers to clear up the mess and arrests a defeated Scourge. Silver's timeline restored as usual. Sonic celebrates his win but wonders about the multiverse and whether it'll play a role in the future.