When officials determine that Gunnery Sergeant Bill Atlas has gone missing, Gibbs (MARK HARMON), Kate (SASHA ALEXANDER) and Tony (MICHAEL WEATHERLY) are charged with trying to find him. Atlas was last seen at Hammersmith’s Country Bar, but his car has been there for five days with no signs of him. At Hammersmith’s, the agents meet sultry regular waitress Vanessa Banta, who helps them realize that Atlas had been having drinks with – and possibly having an affair with -- newspaper reporter Carol Powers. Questioning Powers, the agents discover that Atlas had been revealing information to her regarding some suspicious deaths, and that he suspected he was the next target.
Delving into Atlas’ military past, the agents interview his commanding officer, Commander Joe Sacco, who offers little help for how Atlas could have gone missing. Clearly the men had an acrimonious relationship and Sacco even believes that Atlas’ past drinking problems could mean he’s simply on a bender.
But the agents next turn up some disturbing information. Three of the men in Atlas’ 1992 unit serving in Okinawa – whom all served then under Major Joe Sacco – have all turned up dead or missing in the last eight years. The most recent casualty is Marine Corporal Mark Cohen, who was discovered under gruesome circumstances, having died while being chained to a wall and starved to death in an underground sewer.
While a cigarette butt near Atlas’ car leads Abby (PAULEY PERRETTE) to determine that he was drugged at the time he went missing, the others piece together a gruesome scenario pointing to Sacco as the culprit who has been kidnapping and killing his victims. Although they can’t find a motive, they believe he is a serial killer who has targeted his men one-by-one, leaving little hope that Atlas may still be alive. With this revelation, Tony tails Sacco, only to end up back at Hammersmith’s, where he once again sees the flirtatious Vanessa, who serves him a ginger ale.
Tony tries to stay out of Sacco’s view, who is seated in the back of the bar. However, Sacco soon leaves. When Tony tries to follow him, he quickly realizes he has been drugged. He soon finds himself in an underground sewer, locked away with a starving, filthy Atlas, who is chained to the wall. Fortunately, as Tony tries to recover, he knows that – always prepared – a knife is hidden in his belt, which allows him to wrest Atlas free. During their ordeal, Atlas relays the story of how he and three of his fellow Marines were responsible for the death of four girls. Four of the men in his unit at Okinawa had orders to go back home and so they decided to have their Filipino girlfriends “shipped” back with them. However, the Marines were unexpectedly all assigned to different ships. Certain that the girls were all on one of the men’s ships, they hoped to be able to rescue them from a locked crate. But all the girls died. Among them was Sacco’s former girlfriend who was then Atlas’. Tony is convinced that Sacco has now decided to exact revenge on the girls’ lives by killing each of the four men in his unit.
When the local police track down Sacco’s abandoned car, Gibbs and Kate are called to the scene near where they realize Atlas – and Tony -- are being held captive. They begin to piece together that Sacco is working with Vanessa. As Tony tries to rescue himself and the injured Atlas, they are met by the true culprit... who is not Sacco after all. Vanessa – who was actually the sole survivor of the girls who had been shipped off – was saved by Sacco at the time. With Sacco’s help, she was determined to avenge her friends’ deaths. However, he has finally realized how crazy she has become and is desperate to save Atlas... until Vanessa shoots and kills Sacco. In her following confrontation with Tony and Atlas, she is determined now to kill them as well. Just in time, Gibbs and Kate arrive to thwart her final act and save their fellow agent.