Along with the two main games, Radical collaborated with two comic book publishers to release a series of comic books detailing the background for the game.
- Main article: Prototype comics
The first series was released with collaboration with WildStorm productions. This series consisted of six issues and the main focus was the story of Detective McKlusky and Ella Garcia. The books also provided the background of Peter Randall, Robert Cross and Elizabeth Greene.
- Main article: Prototype 2 comics
The second release is in collaboration with the Dark Horse Comics. This series has been split into three issues, each detailing different stories and bridging the narrative gap between Prototype and Prototype 2.