Gibbs's team is sent to investigate when the body of a sailor is found on board the USNS Chimera, a top-secret naval research ship sailing in the middle of the ocean. After boarding the ship, they find it completely abandoned except for the dead man. Things go from bad to worse when Ducky determines that the dead man died from viral hemorrhagic fever with Ziva suspecting that they're not alone and that someone else is on board although there might be another person on board as well. A secret is lurking on the ship and it's one that might end up costing the NCIS team their lives.
Cmmdr. Skinner's behavior indicates that he has no idea that the Chimera is really just a carrier for a stolen nuclear weapon. Even at the climax of the episode, when Gibbs insists on being told what he is looking for, Skinner breaks down and says that it can fit "into a vial." He really believes that the vessel is being used for bio-warfare research. The crowning irony of the episode is that Skinner, who so arrogantly insists on keeping everything secret from NCIS, has not himself been "read in" to the Chimera's true purpose.
Skinner is played by Steven Culp, known for his recurring role on JAG (series), NCIS's parent series, as Special Agent Clayton Webb.
Requiem (episode) was supposed to be the series' 100th episode, but the producers decided to air "Chimera" instead because the 100th episode's airdate fell on Halloween, and they felt "Chimera" was a darker episode, more thematically appropriate to the occasion.
The episode's plot was based on the story of the supposed "ghost ship," the Mary Celeste a ship that was discovered at sea by the vessel Dei Gratia, with no crew and no sign of life. As with the Chimera, there were plenty of supplies and the cargo was intact, and no clue as to what had happened to the crew. It was believed that, for some reason, the captain and crew had suddenly abandoned ship and been lost at sea. The scene where Tony finds a letter to a crewman's wife or girlfriend that was abandoned midway through its writing, is a tribute to a similar letter found aboard the Mary Celeste, indicating that whatever caused the crew to abandon ship happened suddenly and unexpectedly.
Tony quips that he'll "take 'Horror Films That Take Place on Ships' for $500," a reference to the game show Jeopardy!. Such movies include John Carpenter's The Fog, Leviathan and Ghost Ship (likewise loosely based on the story of the Mary Celeste).