One of John's old nemeses steals an arsenal of nuclear warheads and a scientist to activate them. John is forced to work with his enemy, Olga Petrovka, in order to destroy them and rescue the scientist. Natalie and Malcolm endeavor to protect John's identity from an FBI investigation.

John breaks the protocol of the Agent X Brotherhood to protect a former lover from members of a Washington D.C.- based cabal intent on taking down the President. Natalie, Malcolm and Judge Thorne work to unmask the members of the conspiracy.

A biological weapon is used in a failed assassination attempt, sending John, Natalie and Malcolm on a frantic race to thwart a domestic terrorist group's plans to deploy a virus on a greater scale.