Sonic is not dead, although his body physically is impaled.  One mistake by Eggman is all it took to bring him back...but once he's alive, there's no guarantees he's the same hedgehog he once was, especially when corrupted and infused by lightning with the powers of the reality-warping Phantom Ruby.  You and Tails haven't found his body yet, but Eggman's damage has already been done and he's turned your hero hedgehog into a ruthless, murderous monster with a longing to kill everyone on Mobius.