VIDEOS:
Alister Azimuth
Though you wouldn't know it until the Final Boss battle. For most of the game, he's on friendly terms with Ratchet, but his uncompromising drive to undo his mistakes is what pushes him into villain territory.
Example of:
Big Bad Friend
Cryptosporidium
Example of:
Anti-Villain
The Black Baron
Example of:
Anti-Villain