Specialisté na nebezpečný odpad objeví v jednom ze sudů rozleptané lidské tělo. Po příchodu Dr. Mallarda z NCIS se ukáže, že někdo tělo rozleptal kyselinou fluorovodíkovou, která se používá na různé účely. V námořnictvu je nejčastěji využívají na čistění kovových povrchů. Má silné leptavé účinky, rychle proniká lidskou kůží, rozkládá měkké tkáně a dekalcifikuje kosti. Mallard odhaduje, že oběť byla v sudu méně než 24 hodin. Podle zbytků oděvů patřil znetvořený muž k námořnictvu. Podrobnou expertízou těla dospěje Dr. Mallard k závěru, že smrt způsobil tupý úder. Podle zbytku tetování na těle mrtvoly se ukáže, že neznámy mladík musel působit na některé z nedaleko kotvících ponorek. Gibbs dá rozkaz svým lidem, aby důkladně prohlédli ponorky a on sám se vybere s Kate na ponorku Philadelphia, která vyplula na cvičnou plavbu.

Jeden námořník je sice mrtvý, ale na žádné ponorce nikomu nechybí. Gibbs má podezření, že ho nahradil někdo jiný, nepovolaný s nekalým plánem.

We find Tony on the phone speaking to an Agent McGee, a case agent who sounds green and needs advice about what to do with whatever he's got. There is banter. Kate knocks over Gibbs' coffee to the sound of background music that would be more appropriate just as the axe murderer appears behind the blonde co-ed. Gibbs looks like he's going to commit murder, and Tony looks panicked. Kate offers to get him another cup; he refuses, saying the coffee down the hall isn't coffee. As they gear up Tony,looking very concerned, says they are in uncharted waters as he has never seen Gibbs without coffee.

Arriving at Norfolk, we meet the fresh young Agent McGee, who is wearing a surgical mask over his face. He's apparently new at this. (But isn't he cute!) Ducky examines the body, discusses the hydrochloric acid, and opines that the body was in the acid less than 24 hours, judging by the damage. Judging by what's left of the clothes, the corpse was an enlisted man; he has a discoloration on his left forearm that Ducky cannot identify, but anyone who knows body art immediately recognizes a tattoo. Gibbs goes to the gate and interviews a gate guard. They know that, with security as tight as it is, the body could not have been smuggled on the base; therefore, he was murdered on base by someone with base clearance. Outside the main gate, a small group of protesters walks in a circle, chanting save-the-whales slogans. That night, Tony makes McGee stay and stand guard over the crime scene before he and Kate leave.

The next morning, Ducky and Abby video conference with the team in Norfolk (including McGee). Ducky confirms cause of death on the body was blunt force trauma to the head. Abby confirms that the mark on the arm is in fact a tattoo - the tail of a dolphin, which tells Gibbs that the dead man was a submariner. Gibbs asks McGee for the number of subs in port; we get some insight into McGee's lack of organization skills as he attempts to locate the list. He comes up with it (finally) and we find that the USS Philadelphia left port this morning. Gibbs wants a copy of the alpha rosters. While this is going on, Ducky is giving a lecture on the history of tattooing over the video conference. Gibbs looks extremely exasperated.

Gibbs, Kate and Tony are walking along the docks, discussing that the body was probably put in the acid to obscure its identity. McGee runs up with the alpha rosters, and tells Gibbs that everyone on all the ships is accounted for - including the Philadelphia. Gibbs wants to talk to the submarine squadron commander. McGee advises that he avoid Captain Veitch, who can be "difficult." Gibbs gets right in his face and asks if McGee doesn't think Gibbs can be difficult. McGee is sure Gibbs can, and Gibbs leaves.

Veitch adamantly denies the possibility that someone could slip aboard a sub as an impostor. Gibbs is equally adamant that the possibility is quite real and must be investigated. Gibbs wants the Philadelphia called back, and Veitch refuses; she is on her way to a NATO training mission. Gibbs says that's fine; he wants himself and Kate transported to the sub to conduct their investigation on board. Veitch kicks up a fuss about allowing Kate onto a sub. Gibbs has Kate leave, and then becomes "difficult." Here we learn that Kate has been trained as a profiler. He gets his way and Kate, after a completely unnecessary show of righteous indignation, goes with Gibbs to the sub. She has a great smile.

Gibbs and Kate take a plane to an aircraft carrier, then a helicopter to a frigate, and from the frigate they take a very small boat out to the sub. They explain the situation to Commander Peters. He will cooperate, but the sub is about to commence an Anti-Submarine Warfare exercise in the Atlantic and he is very interested in winning the bet he has with the opposing sub captain. In her lab, Abby works on building a computer model of the dead submariner. She has examined his stomach contents and determined he had a Big Mac and fries as his last meal (and she now knows the composition of McDonalds Special Sauce). Back on the sub, Gibbs and Kate are interviewing their five suspects.

They begin with Petty Officer Drew, who does not know his right from his left and claims to be from South Boston but has no accent. They move on to Petty Officer Thompson, who claims he graduated high school a year late due to mono. After the interviews, Kate and Gibbs have found nothing. Gibbs quizzes the skipper about how the ship could be harmed from the inside; there is a laundry list of ways. The skipper wants them gone; Gibbs says they'll leave when they're done. In her lab, Abby has finished her computer model; he does not look like any of the suspects. She emails the picture to Tony for him to show it around on base in Norfolk. McGee asks Tony what Abby looks like, despite having seen her on the video conference the day prior. Tony tells McGee in no uncertain terms that Abby is out of his league because McGee has no tattoos nor the urge to get one on his buttocks.

On the sub, the sonar has located their target. Gibbs and Kate are certain that the impostor is on this sub; it is the only thing that makes sense. They further deduce that the accomplice must have altered the service record before arriving on the sub; he either worked in personnel or has an accomplice. Gibbs demands that the sub be taken to periscope depth so he can contact Tony. He passes on his suspicion about the service records and sends Tony to investigate.

Ducky comes to Abby with good news and bad news: no DNA match on the body, but Gibbs' theory of altered service records is a good idea; Abby can check crew photos of the five suspects' previous postings. Tony and McGee check out personnel; McGee saves the day by recognizing that if the impostor was working in the personnel office, he would have quit before taking up his fake posting. He learns that Joshua Fox quit recently. On the sub, Gibbs is pushing water down Kate's throat for some reason. Then he sends her to the bathroom to distract the COB, 'unhydrate' is the word he uses, and let him sneak out to question a suspect again. She points out that he could have just asked, and goes, allowing him to escape.

Tony and McGee drive out to Joshua Fox's address and break in to investigate. Gibbs goes to question PO Thompson, who lied about his extra year of high school. Thompson admits he wasn't home sick; he was in juvie. The record was sealed, but Thompson was afraid if the Navy learned of it, he'd never get posted on a sub. Gibbs is caught by the COB and dragged back to the wardroom with Kate. Abby has no matches on the photographs; Ducky gives her a hint by using the word 'absent.' Tony and McGee discover that Fox is an anti-sonar whale-hugger activist and has been developing a tiny canister to deliver sarin gas into a sub's air conditioning system.

Tony gets an emergency message to Gibbs on the sub via low-frequency transmission, advising him of the threat of sarin gas on the ship. The skipper reads it, sends for Gibbs and Kate, has the air conditioning turned off, and orders the ship to surface in an emergency blow. Kate is thrown into Gibbs, who is up against the wall; they hang onto one another for dear life. All the shippers can be heard sighing into their handkerchiefs. The COB comes to get them and they head for the bridge. In her lab, Abby identifies the dead submariner as Petty Officer Drew, who was absent the day the crew picture was taken and had to be in a make-up photo.

On the sub, Drew, who knows he's done for, asks permission for a head call. He leaves as Gibbs and Kate arrive and receive their first message; just then, a second message arrives from Abby identifying Drew as the impostor. The skipper hands it off to Gibbs and Kate, who go looking for Drew. In what may possibly be the fastest suicide ever, Drew has gotten out of his uniform, into his bunk, and suffocated himself with a plastic bag in the space of what might be thirty seconds.

Tony passes the information about Fox and the eco-terrorists to Gibbs. The skipper is heading the sub back to Norfolk; they submerge because subs are faster underwater than on the surface. The ventilation system must remain off due to the continued gas threat; the canister has not been found. Tony returns to D.C. and brings the canister prototype to Abby. She asks about McGee. She also determines that the canister has a bi-metal trigger, which is set off by either extreme heat or extreme cold. This particular canister responds to cold - a temperature of five degrees centigrade, to be exact. On a sub, the air conditioner system or the freezer could be cold enough to trigger this canister.

On the sub, Gibbs is bugged by the lack of sarin gas release . Kate blows it off - "He never had a chance"- but Gibbs doesn't buy it. Why would he commit suicide before he could release it if he knew he was going to die when it was released anyway? The conversation is interrupted by the arrival of ice cream, which might as well be eaten because it will otherwise melt; it had to be taken out of the freezer to make room for the body. This is standard operating procedure on a sub - which the fake Drew would have known! Gibbs goes quickly to the freezer, realizing the fake Drew booby-trapped himself. They open the body bag to find that the gas has already released - inside the corpse. He swallowed the canister before committing suicide. Gibbs and the COB carry the body down to the torpedo room and stuff it into a tube. Kate has run to fill in the skipper, who calls down to the torpedo room with permission to fire. They do so, and live to fight crime another day. And the ice cream is saved also.

Back at HQ, there is banter until McGee arrives with his final report. Tony asks if McGee didn't learn how to use email at MIT. Kate is surprised - "You graduated from MIT?" Gibbs adds, "And Johns Hopkins." McGee is a brain. Then Gibbs asks why McGee is in D.C., and McGee announces that he has a lunch date with Abby. Tony, amused, offers to take McGee to her, reiterating that McGee is not Abby's type. McGee refers back to the "urge" Tony mentioned before (tattooing his buttocks) and states that he took care of that; he went with "Mom." Tony is left speechless as McGee gets in the elevator to go down to the lab.

Kate and Gibbs watch from their desks; Kate wonders what McGee said that left Tony speechless, and Gibbs replies, "He told him he got a tatt on his ass." Gibbs walks away, and we watch Kate watch the elevator, a speculatively sexy look suddenly crossing her face. Clearly, Kate is intrigued. As are we all.