After the arrest of Vaughn six months ago, Michael has been working with the CIA, to capture and execute all the people that burned him from the organization. There is only one high operative remaining. When an attempt is made to capture the spy, he decides to commit suicide as an alternative to facing the CIA. When Michael shows up to debrief, he finds Max bleeding on the floor. He attempts to chase after the murderer in vain. Michael is being framed for the murder since the box of ammunition used in the murder weapon is found in his car.

An intricate bomb is set to kill Michael, which is eventually tracked back to a Romanian war criminal. The Romanian confesses that he made the bomb for Tavian Korzha, an old friend. They track down Tavian to his warehouse, but he escapes. Using a computer at the warehouse; the team tracks down Tavian’s source of funds. However, Tavian sees through the attempted ambush; he kidnaps Sam and demands for a meeting with Michael on an island. The FBI and NSA manage to lock down the island. When Michael returns to his loft later, he meets Agent Pearce, who has evidence that he killed Max. Michael is arrested at gun point and taken away. Agent Pearce is eventually convinced by Jesse and Sam, to let Michael meet Korzha. Korzha is convinced by Michael, to confess to framing him for murder while he is wearing a wire. However, to avoid being investigated, Korzha kills himself and Michael is exonerated.

Anson and Michael are kidnapped by Larry Sizemore, who wants Michael to break into the British consulate and steal some information. Later, Michael is forced to start working for the organization again. Anson wants Michael to erase any information that the CIA has on him and the organization.