A woman Marine first lieutenant, born in Kuwait, who has served in intelligence, returns from Iraq and turns up dead in a motel room in a small town; Gibbs and company investigate, with both help and resistance, and find three bad guys.
Responding to a call, Gibbs and company find the body of a Marine major in an underground utility vault beneath a street intersection. Abby finds the cause of the death, and Gibbs and the gang find Sharif, the bomber from the golf course.
A couple find the body of a Navy petty officer in an abandoned restaurant in Georgetown; the Metro PD calls and helps the NCIS; Gibbs and company investigate. Messages leave clues leading to an exclusive nightclub. The gang figure it out.
A Navy lieutenant, a member of an international nuclear-inspection agency, asks Gibbs to solve the officer's own murder because he knows that someone has exposed him to radiation poisoning.
A family crypt in a mausoleum explodes when unsealed; Gibbs and company investigate; Ducky says that parts of at least three skeletons occupied the vault. The team identify and check out a suspect, and Gibbs and Hollis get a major surprise.
Someone attacks a Marine corporal and leaves him to die, facedown in a snowbank in a park; Gibbs and company investigate. Mike Franks shows up and takes part; he and Gibbs sort it out and work it out. Tony and Jeanne encounter a problem.
An explosion kills two NCIS agents from another team; Gibbs and company investigate; feelings and emotions run high. Ducky and Abby find evidence suggesting opposite answers, but the gang resolve the problem, and they solve the case.
Gibbs and company investigate a crime scene; while doing so McGee recognizes that key details duplicate details in his second novel, still unfinished and in progress. The gang find two bodies; they eventually find the delusional bad guy.
Jen meets with an informant about the Frog, but someone kills the witness; Gibbs and company investigate. Jen obsesses about catching the Frog. Abby produces many answers; although the gang persist, they find a surprise but no Frog.
A blind photographer takes a picture; his assistant sees the body of a sailor in the background, and she calls the NCIS; Gibbs and company pursue. The gang find a second body, which leads to another crime, three solutions, and the bad guy.
While Jen attends a conference in Paris, Gibbs serves as the acting director. When a taxicab delivers a fare to the NCIS headquarters, the passenger, a Yemeni, is DoA; the gang investigate. Jen diverts to Moscow, and many answers emerge.
Jen returns from Paris; at home she finds a curious sight. All NCIS agents in Washington must take polygraph tests; Gibbs and the gang look into that. Tony and Jeanne deal with an injured pedestrian; Jeanne introduces Tony to her father.
Tony meets Jeanne's father; Tony excuses himself to move his Mustang, which explodes while the gang watch; Ducky says that the victim is not Tony. The Frog meets Jen, but she lets him leave; Gibbs and others pursue him but arrive too late.
The NCIS gang investigate the death of a sailor in a hit-and-run wreck, which turns into a shoot-and-scoot; Ducky finds nearby the body of a young woman who gave birth and died before the wreck. The team figure out the lies and the case.
A Captain is killed at home with a spear. His wife is having an affair with his Major, whose prints are found at the scene. Jethro's ex-wife, Stephanie, is seeing the Major too. Lt. Col. Mann, Jethro's girlfriend, leads the investigation.
While demonstrating an autopsy, Ducky announces murder; Gibbs and company investigate. The victim worked for the FBI, which tried to catch a person who erased old identities and created new ones. The NCIS and the FBI catch the bad guys.
A Navy lieutenant threatens to jump from an 11th-floor ledge in Washington; the Metro PD calls the NCIS; Gibbs and company respond and investigate; Gibbs talks the man out of jumping, then someone shoots him. With help the gang find a mole.
A special friend of Gibbs's daughter asks for help with a Marine sergeant, who has begun stalking her. Gibbs gives him the word, but soon someone abducts the friend and tortures and kills the Marine. Gibbs and Tony solve it and work it out.
While a Navy rear admiral rides in a taxi, two motorcyclists, using silenced pistols, execute both men; Gibbs and company investigate. Ducky says that the target was the driver, who was a political refugee from Burundi. The gang solve it.
While McGee gives his den of Youth Rangers a tour of the NCIS headquarters, one of his boys pops up in a missing-persons database; Gibbs and company investigate. The team find lies, deception, a fugitive, a new murder, and the real killer.
A to-be-decorated Marine, Corporal Damon Werth, becomes violent during his PTSD treatment. He has fistfights with NCIS agents. It is found that he is on steroids, and a Navy contractor is suspected of experiments on him.