In the game, Prophet rescues a dying Alcatraz during a submarine explosion and then combines Alcatraz with his suit before committing suicide to prevent a Ceph virus within himself from spreading, and also to allow the Nanosuit to fully bond with Alcatraz. Throughout the game, various references and flashbacks relating to Prophet's past between 2020 and 2023 can be heard. He later appears in the end of the game where he talks about the Ceph and the things Alcatraz accomplished.
