User blog comment:JokerJay779/Sonic Mega Bros./@comment-17720060-20130606231713/@comment-6576725-20130606235117

Well you see the villans came back because of the events of the first saga with the Genesis Generator and the Space-Time disturbances it created. It allowed portals to open up in the Underwhere where all people who games are over go allowing old fallen foes to return. Mephiles is an example since he was wiped from existence.