On the naval base in Norfolk, a ghastly discovery is made: a decomposing body amid the liquid inside a toxic waste drum. However, as Gibbs (MARK HARMON) and the others are called to the scene to investigate, Ducky (DAVID McCALLUM) determines that the body has been dead for less than 24 hours. While radical animal rights advocates protest on the base for better treatment of whales, the NCIS unit gets to work with the help of the base’s NCIS Special Agent McGee. A partial tattoo on the victim leads Gibbs to believe he’s a submariner and four subs are accounted for on base. However, a fifth, the Philadelphia, left dock this morning. While everyone on the subs’ crews is accounted for, Gibbs believes that one of the crew members on the Philadelphia may be an imposter, who killed the victim to take his place on board. With five new crew members on that sub, Gibbs and Kate (SASHA ALEXANDER) make a rendezvous with it to interview those men. But, when they do, none of them seem particularly suspicious.
While they wait for the DNA registry to help identify the body, Ducky and Abby (PAULEY PERRETTE) try putting together a visual image of the victim’s face. And Gibbs perseveres, working the angle that someone would want to harm the boat from the inside. When he realizes that the fingerprints of the five “suspects” match records from the Norfolk personnel office, he deduces that one of them has an accomplice in that office. As Tony (MICHAEL WEATHERLY) and McGee investigate Gibbs’ hunch about a personnel employee, Ducky and Abby work to get photos of the five crew members from an independent source. They believe that one of the crew members’ photos will match their victim’s face and, if so, they will determine which man aboard the Philadelphia is being impersonated. At the personnel office, Tony and McGee discover that one of the employees, Joshua Fox, quit two days ago and decide to follow-up on his whereabouts. Procuring his address, they discover an abandoned home with one very scary feature: an eco-terrorist war room complete with photographs and schematics of nuclear submarines. Scouring for information in the room, McGee, who has a degree in bio-medical engineering from Johns Hopkins, determines that Fox is planning to somehow introduce sarin gas into a submarine’s air conditioning system — which would kill the entire crew.
Tony relays the information to Gibbs and, while the sub safely checks out for now, he knows that time may be running out. And, with Ducky and Abby finally able to match crew members names’ with faces from photos on the men’s other ships, they do indeed identify the imposter as one of the five new crewmen: Petty Officer Drew, who is actually former Petty Officer Sean Travis, dishonorably discharged and working with Joshua Fox. Travis and Fox are part of a small three or four man cell of radical eco- terrorists concerned about whales. But when Gibbs and Kate go to detain Travis on the sub, he has committed suicide... and they can’t find the small canister of sarin they learned that he supposedly had in his possession. As long as the canister remains sealed, all those aboard the sub are out of danger. Still, Gibbs is troubled. He then realizes that they are still, in fact, not safe: Travis’ body has been put in the freezer to keep preserved until they return to Norfolk, and Travis has actually, posthumously put a back-up plan in motion. Gibbs believes that Travis booby-trapped himself, ingesting the sarin gas canister which was designed to be triggered by cold. When his core temperature drops to the trigger temperature, the deadly gas will be released.
Acting on that ominous theory, Gibbs and Kate find a bagged Travis in the sub’s freezer, and see that his abdomen is distended and growing, a sign that the sarin has been activated. Working with crewmembers, Gibbs and the others jam the body bag into a torpedo and jettison it from the sub... where it, fortunately, drifts harmlessly toward the surface.