Šestý díl seriálu začíná v lodní jídelně. Jednomu z námořníků se udělá nevolno a za pár minut umírá. K případu je povolán vyšetřovací tým NCIS, který má začít vyšetřování na lodi. Když však dorazí na místo činu, na palubě nikoho nenajdou. Na lodi chybějí záchranné čluny - všechno nasvědčuje tomu, že byla velmi rychle opuštěna, dokonce bez toho aby vyslali třeba i jen S.O.S.

Při pátrací akci objeví McGee velmi dobře vybavenou laboratoř, podle všeho ji využívali na zkoumání potkanů. Tony, Ziva a McGee objeví krvavé stopy které je dovedou k mrazícímu boxu, ve kterém najdou tělo mrtvého námořníka. Zjistí, že zemřel v důsledku virové hemoragické horečky, které byla vystavena celá posádka.

Gibbsovi je jasné, že nemůžou opustit loï. No Ducky poznamená, že to je jejich nejmenší problém. Pokud je jeho diagnóza správná, do rána budou mrtvi...

In the squad room, bored agents sit at their desks, awaiting Gibbs' call but nothing happening. Abby arrives, full of joy at the prospect of their collective evening out at the Brain Matter concert (Abby's friend's band). All the team had promised to go with Abby to the concert. Suddenly Tony and Ziva have things to do. Tim is not permitted to back down on the concert: Abby threatens him with her dog collar stud bracelet. Gibbs arrives in the nick of time to save our Timmy from earful hell, and offers him seasick hell instead. The ship Chimera has a dead sailor. Tim checks the ship...it is not on the navy register. Abby is not amused to be deserted by her concert-goers.

Team goes to get the helicopter. They are told "go in, get the body, come back" by the Commander. No other investigative agency has clearance to get on the Chimera and even NCIS has no authority to investigate what's on the Chimera. The commander wants to prevent them taking their camera and they are not to treat it as a scene to be documented. Gibbs just says bring the camera so they do.

They fly to the ship by helicopter. No-one is there to meet them. Ghost ship. The helo has to know whether the team is staying or going. Gibbs says "we're staying".

Team enters the "highly sophisticated top secret ship" that looks like a tramp steamer. The lights are on but no-one's at home. Right ship, wrong night. Everywhere they go, it's empty but it's as if everyone had just paused for a moment. Tony notes that in the poker game, someone folded when he had a full house. Ziva finds an unfinished letter which mentions that if their dive is successful they might come home soon but....and the letter stops mid-sentence.

Gibbs and Ducky are wondering why no distress signal was sent. Lifeboats are missing. Ship was abandoned. Too much of a hurry for a mayday? Ducky admonishes Gibbs reminding him that the Commander had warned them not to ask any questions beyond their pay level.

McGee is heard retching...comes out and mutters "found something". They enter a room and WOW...it is high tech. Rats in cages. It is a big-tech, mass spec type lab. It is for looking at stuff not visible to the naked eye.

Tony and Ziva and McGee are sent into the hold to search. Tony sings Black ship black ship have you any .... It is a black ops black ship that is a govt.secret. They are spooking each other.

Rats spook Tony: Pneumonic plague has put him off them. Ziva can hear things. She declares she does not "believe" in ghosts. She says what a Chimera is (monster): they did not name the ship "the puppy". They all approach with caution, open a door and Gibbs says "boo! Get in". They are in the galley/mess room. Ducky spots the coffee-ground emesis from the dead guy's severe internal distress but they don't find the body. Tim is looking very green around the gills (seasick in the presence of vomit).

Ziva spots footprints. They follow the lead. They get to a cold store and find the body. Ziva can feel that there is something/someone alive on board. Ducky notes the dead guy in the freezer room shows signs of petichial hemorrhaging. Maybe it's a sign of asphyxia but he needs to run tests. So Gibbs tells Tim to give him a satellite link. They try to contact Abby but she is listening to Brain matter and cannot hear them. McGee yells til she hears. McGee reports that Tony is dealing with his phobia about rats, Ziva with her phobia about ghosts, McGee with his seasickness and Abby asks what Gibbs is dealing with? He gets in front of the camera and says "them".

Jen arrives in Abby's lab. Gibbs reports the dead crewman: Dr Satoshi Takata, marine biologist, PhD in Biology from LSU, navy officer. Ducky thinks that the COD was viral hemorrhagic fever to which they have all been exposed: it is fatal to anyone exposed to it so if Ducky is correct the team will be dead by morning.

Jen talks to the commander via MTAC. He won't divulge what the ship was doing. Jen argues. Deadly virus outranks top secret ...commander disagrees. He stonewalls. She threatens to go over his head.

Ducky and Gibbs are doing the autopsy using an electric knife. Tony is mucking up all the equipment as he tries to do Abby's work via remote instruction from her on satellite phone. He is doing the gas chromatography tests. While they wait for that to process, they do the blood tests. She talks him through it all. Tony inhales the specimen before Abby warns him on no account to inhale the specimen. Tony gets paranoid that he will die. Ducky speculates that rat bites might be the cause of the navy man getting the virus.

MTAC patch through Ducky to the commander. Ducky decides to quarantine the ship and the Commander is unhappy in the extreme. Jen gets stroppy with the commander and asks for the mission to be divulged. He says no. So she orders her team to investigate. Commander says no: she says you can't stop me. Commander says he can't read her in over MTAC. So she says come here and turns off the MTAC screen.

Team meeting. Searching the ship is discussed. The team are spooked. They leave Ducky with the body and a walkie talkie but Ducky is just normal and chats to the body, as ever. They go looking for anything: Tony is getting paranoid. He is sure he is going to die and has found a dark spot on his hand (Ziva insists it is a freckle he has always had). They argue hard. Gibbs radios to Ducky and asks for the list of symptoms for the deadly disease. Ducky reports to Tony what are the symptoms...matches Tony's grumbles. He is really sure he will die. In a discussion with Gibbs about how to die (Gibbs suggests "silently") Ziva runs off. They chase her. She was sure she saw something running. They find a biohazard room. And a dead rat. And then the power goes out. So they use torches. Now it is dark and spooky.

Gibbs and Ziva find Tony and the rat. They hear bumps. It is McGee. They want McGee to get the electrics working. Ziva finds the room and out comes a scared guy. She was right. He is the cook. Why were you hiding, why did the crew abandon ship? Cook says it was that thing they brought out of the water that Takata was working on. Takata puked blood on the cook so when they abandoned ship, they wouldn't take the cook with them as he was contaminated. He says then someone else was on the ship and hit him unconscious and he thought the NCIS team was the "someone". He is a very frightened cook.

McGee and Tony continue trying to fix the electrics. Tony is freaking as he thinks this is his 3rd round with death and these things run in 3s. McGee just says, ok, until you are dead, please help me fix the electrics. So Tony does. They find batteries, and he has calmed down.

Jen is being read in on the biohazard warfare testing which is illegal. The commander tries to charm her into complying with his wishes. She resists softly but effectively and demands he fly someone to the ship to film it from above.

Life jackets signalling transponders are lacking their batteries. Someone has done sabotage on the ones who fled the ship: Tony and McGee are grim.

Ducky has found that Takata was drugged and injected with the virus. The rat bit him and died. It is not airborne virus. The team is safe from bio harm. The lights come on. They praise Tim and find that he did not fix the lights. Ziva is sure someone else is there. Gibbs agrees because he spots a signal light on the deck that wasn't there before. They are nearly killed as they examine the light because a net-load of barrels hurtles down on them, but they catch Lieutenant Ferris, the communications officer. He warns them that they will die, but not from virus. They arrest him.

Jen and Commander in MTAC tell Gibbs that pirates are heading for them...they saw the boat. Gibbs demands to know what the pirates are after: he is told that it is a vial of untested stuff. Tim comes and says they cracked it, as they found negative pressure storage...Gibbs barges in. Tim worries about him being contaminated. Gibbs lifts lid on a modern steel chest and looks grim. Ziva reports assault craft is 5 minutes away.

The team starts doing tasks, loading guns, Ducky mixes up red stuff in a beaker, Tim is purposefully going somewhere on the ship.

Daylight bright deck, so time has elapsed: Russian pirates searching. Ziva confronts a pirate and knocks him down. Gibbs escorts Ducky through the ship.

Other pirates are searching. Pirates find Lt Ferris (who the team had arrested) and he holds a note in his hand: "airborne virus on ship". Pirates confront each other: they want to leave and the boss says no. He aims a weapon at his own men. Pirates find the guy that Ziva knocked down. Boss realizes that there are people on board and checks whether his boat is still there: it is not. He says "bastards" (in Russian). He says it again.

We see Gibbs and the team on the little assault craft and the team explain to each other what happened. Tony holds up papers he has found which are Russian: Gibbs reads them and says Russian navy orders. Ducky reports that Ferris will wake in 2 hours and have a hard time washing off the fake blood. Tim says he has doctored the ships navigation systems so it sails in a circle. Gibbs tells Tim to open the chest: he finds nuclear warheads. So McGee ponders aloud that it was Russian navy recovering nuclear weapons that US Navy didn't think that the Russians knew that the US had found.

Ducky says maybe they should tell the navy that the Russians are on the Chimera and that the team are on the pirate boat. Then they see a missile hit the Chimera and blow it up. Ziva asks "how did they know we got off the boat?" and Gibbs answers, "Don't think they did."