This won't be easy for Sonic the Hedgehog fans to hear, but he was murdered.
In The Murder of Sonic the Hedgehog, a free visual novel released by Sega today, Sonic is the victim in a murder mystery birthday party for Amy Rose. He's not just pretend murdered, though: he really gets knocked out.
But is he dead, for real? You'll have to play the game to find out. I did, and it's pretty good for a freebie. The detective work is just on-rails 'collect the evidence and then confront suspects with it' stuff, but the 2D ring-collecting minigame you play to 'think' is entertaining, and even slightly challenging near the end.
Regarding whether or not the game is canon, Sega says, "You know what they say: everything is canon," but adds that The Murder of Sonic the Hedgehog "is not a Sonic Team title."
They "strongly believe in the power of headcanon," however, and I take that to mean that, whatever happens in the game (I'm not saying), Sonic can be dead if we want him to be dead.