Peter Klein was an undercover CIA operative.
Season 3
Peter and his partner were both seen walking inside of an elevator when an agent of The Covenant planted a device on the elevator that made it descend nearly to the ground floor. However, the elevator suddenly began to ascend and, unbeknowst to the agents, they were being air-lifted by a Covenant chopper.
Klein and his partner were later seen inside of a building tied-up and gagged. A couple of Covenant thugs grabbed Klein and sent him into a torturing room, headed by Oleg Madrczyk. The thugs held him down as Oleg approached Klein with a large cleaver.
It was later confirmed by Sydney Bristow that Klein had been decapitated and his severed head was placed in a box. Along with his head were a set of instructions sent by the Covenant, which were implanted in Klein's mouth.