After the events of Crysis 2, Prophet's personality, stored in his Nanosuit, assimilates and takes control over Alcatraz's body. Joining with Psycho and a team of elite Nanosuit soldiers, he travels around the world looking for the Alpha Ceph from the knowledge he gained about Ceph existence during the events at Lingshan islands. One by one his team loses interest in the hunt believing that all Ceph are destroyed, until Prophet and Psycho finally trace the Alpha Ceph in Siberia, Russia, only to be disabled by C.E.L.L. using K-Volts. C.E.L.L., now in search of global domination of land and technology, betrays all the remaining Nanosuit soldiers and starts skinning their bodies out from their suits so as to recover the lost alien technology. Everyone involved in the Nanosuit program were either recruited or detained by C.E.L.L., including Scientists Nathan Gould and Claire Fontanelli. C.E.L.L. runs out of Nanosuit soldiers to skin for alien technology that integrated with their suits, so the transfer of Prophet to the facility was requested. Locked in a storage device with powerful EMP shocks to keep him dormant, Prophet is transported to the nanodome in New York City by C.E.L.L. However, Karl Ernst Rasch comes to know about the corrupt intention of C.E.L.L. and resigns from the post of CEO of Hargreave-Rasch Biotechnologies, deletes all the research done by him and Hargreave of Ceph Technology so as to stop C.E.L.L.
