McNulty and J.T. mount a rescue mission in remote terrain in the Philippines to save a captured Navy SEAL, who was written off as dead three years earlier. The operation is met with numerous obstacles, however, including resistance from the Pentagon's civilian-oversight board.

J.T. and company scramble to thwart a bioterrorism plot when it's discovered that the plague is being produced in an illegal lab. Meanwhile, J.T.'s relationship with Samantha is tested when she receives an appealing offer.