A naval officer dies on board Air Force One of an apparent stroke after eating with the president. Secret Service, F.B.I. and N.C.I.S all want to take charge of the investigation to determine if it was murder or natural causes.

A marine dies during a training jump. His parachute was sabotaged. NCIS tries to determine who did it. When they run into a legal issue, they call on Lt Bud Roberts from J.A.G.

A sailor is killed in an apparent drug deal gone bad. NCIS investigates to clear the sailors name.

The NCIS team investigates world of online gaming after a reconstruction of a video game stunt gone bad, kills a sailor.

The mummified remains of a sailor is found by a hunter. The sailor had been accused of stealing millions of dollars, but the money was never found. NCIS investigates to determine who really stole the money.

After a sailor is found naked in a freezer, it is determined that he is suffering from long term drug use. But his recent drug test showed no signs of drugs. An agent who used to work for Gibbs calls on him for help to figure out if how he beat the drug screen.

A badly decomposed uniformed male body is found in a barrel of hydrofluoric acid on a naval base. His skull was fatally struck with a blunt instrument. A partially preserved tattoo indicates a submarine crewman, yet none is reported missing, so NCIS suspects the murderer took over a sailor's identity after killing him. Leroy Jethro Gibbs and Special Agent Caitlin "Kate" Todd, most (un)welcome as unprecedented female on board, conduct an investigation on board the sub Philadelphia, on NATO exercise in the Atlantic, to find out about five possible suspects among the fifteen new crew members, including sonar Petty Officer Drew and Petty Officer Thompson, who lied about missing a year of high-school because of juvenile detention. The captain, Commander Robert Peters, is unwilling to keep them isolated as he can't spare time or anyone during the strenuous exercise, but sabotage is a real danger, probably within 48 hours as that time frame suffices for DNA identification. The roughly reconstructed face doesn't resemble any of the five, nor do their fingerprints turn up anything- the service personnel files must be doctored; Ducky thinks of looking for crew group photographs from ships they served on- still no match, but Abby Sciuto thinks up one better. Meanwhile on land, Anthony DiNozzo and his apt pupil Timothy McGee examine someone who suspiciously left the base recently, who turns out to be a whales-obsessed eco-terrorist with a terrifying use for chemicals on board...

A translator from Gitmo dies with emeralds in his stomach. NCIS investigates to find out which prisoner smuggled them in, and what he's after.

A marine widow receives a phone call from her "dead" husband on the day of his funeral. NCIS investigates to determine if it was a crank call or if it was really him.

A Jane Doe crawls out of a shallow grave in a park, with virtually total amnesia caused by a blow on the head and the emotional trauma of live burial, unlikely to recover fast or completely, yet tells the police, which calls the NCIS, about a bomb on an unspecified US Navy ship. She wasn't raped but gets memory flashes, first about a church. She pretends to recall her name and address to grant the permission to leave the hospital, and then is taken in by Caitlin 'Kate' Todd who keeps trying to trigger her memory about the bomb. A magnetic hotel key and the chemicals required for a serious explosive are found in the grave. Micro-laser numbering traces the key to the Jackson hotel in Washington, notably Mr. Walter Richter's year long-leased suite; it contains his corps, fitting Jane Doe's description of her attacker, but he is dead too long and worked for a German bomb detection equipment company...

A naval officer is killed on base on the beach. There are 2 witnesses to the crime, a sunbather, and a spy satellite that was watching the sunbather.

The severed leg of a Marine is discovered. The investigation takes a turn, when they discover the victim had already "died" a few years ago.

When a Marine Recruiter is killed by a sniper, NCIS starts to investigate. When another recruiter is killed in another area, the FBI tries to take over the investigation. It's a race to find the sniper before another recruiter is killed.

The body of a naval dentist is found bound and gagged alongside the road to the base. NCIS investigates with the help of a local Sheriff. As more people are killed in the same manner, they start searching for a serial killer.

Gibbs's former military C.O. is wanted by the F.B.I. Gibbs tries to find him first, and shuts out his team. But his agents stand by their Boss.

A terrorist manages to infiltrate NCIS HQ. He takes Ducky, Gerald and Kate hostage. It's up to the rest of the team to find out what he's after.

A body falls out of the ceiling during a rave party. The victim was dressed after he was killed.

A seal convicted of murdering his wife escapes from prison. He claims to have discovered who really killed his wife, and wants revenge. To catch him, NCIS must reopen the case, to figure out who he's after

An NCIS agent is murdered while tracking down a lead on a cold case. Now the team continues the investigation to find his murderer.

A marine disappears, a further investigation shows that other members of his former unit have been reported missing, then found after they were tortured/killed. Can they find the marine before he becomes the latest victim?

A marine is killed with a rocket launcher. This leads to an investigation of Weapons trafficking. NCIS works with and ATF agent to get the Arms Dealers, and the Militia who was going to purchase them.

A Seal is killed in an apparent accident while training for a highly classified mission. NCIS investigates is discovers that it wasn't an accident. NCIS must quickly determine who killed him, or the mission will have to be aborted.

As Gibbs's obsession with the unknown terrorist hits its boiling point, the terrorist returns. Taking Kate hostage, he's on a mission to assassinate the President's of the U.S. and Israel. All is not as it seems though.