10 Times Main Characters Killed Each Other
4. James Heller Killed Alex Mercer - Prototype 2
The first Prototype game revolved around an amnesiac shapeshifter named Alex Mercer, while the sequel puts players in the shoes of ex-U.S. Marine Sergeant James Heller.
Heller isn't just a new protagonist - he's got a special bone to pick with Mercer, who he blames for the death of his family during a new outbreak of the Blacklight virus.
More to the point, Heller is himself infected with a strain of the virus which allows him to go toe-to-toe with a super-powered Mercer, leading to an epic battle at game's end.
Heller eventually manages to subdue and defeat a maniacal Mercer, finishing the job by consuming his essence and absorbing his memories, in turn saving the day and becoming the new dominant force on Earth.
The anti-hero-to-villain pipeline may not be all that original, but having the new main character basically ingest the old one is definitely a neat trick.