The pilot that aired few weeks after the show's premiere, was aired as a JAG episode, but also a pilot titled "Navy NCIS: The Beginning".

While on Air Force One, a Navy Commander dies. Agents from NCIS decide to take the investigation into their own hands and also force Secret Service Agent Kate Todd to help. Now the NCIS team has to figure out if the Navy Officer's passing was of natural causes or not.

During a training exercise, a marine's parachute fails to open and he crashes into a parked car where two teenagers were making out. The NCIS team heads to the scene and has to determine if the marine's passing was accidental or a cuddle.

When a Navy commander's body washes up on shore along with the bodies of two drug runners, Gibbs refuses to believe that the sailor who washuged was dirty.

The NCIS team investigates when a seaman's body is found at the bottom of the sea in his dress whites, with a ceremonial sword. They discover that he was addicted to a Wizards and Warriors style role-playing game. Now, the team must figure out how involved he was in the game and how far he would go to get revenge on his arch enemy, another sailor.

A Navy lieutenant who was reported missing nearly ten years ago has been found by a deer hunter. When the NCIS team arrives at the scene to investigate, they see that his remains have been mummified. Now, they have to find out what happened to him and what happened to the one million dollars that he had on his ship.

An NCIS agent who used to work under Gibbs asks for the team's help investigating a case where sailors on an aircraft carrier are dying of a drug overdose, but have no history of any kind of drug abuse.

A decomposed body is discovered in a tub of acid at a naval base and Ducky and Abby learn that the victim was a submariner. Gibbs discovers that there have been no reports of a sub crewmember missing, so he deduces that one of the subs has an imposter on board. With this new information, the team must find out which sub the man posing as the victim is in and what intentions he may have towards the sub.

The NCIS team head to Cuba to investigate a Navy translator's connection to smuggling at a detention center after he suddenly dies at the wheel of his car when returning to the U.S. from Guantanamo Bay.

After a marine widow receives a call from her dead husband, the NCIS team takes on the case and has to exhume the body to deduce whether the call was a prank or not.

After being buried alive, a woman comes out of the grave with amnesia and the only thing she remembers is that there is a bomb aboard a Navy ship. While trying to help Jane Doe recover her identity, the team finds out that not everything is what it seemed at first.

When a Navy commander, who was a technical advisor to a civilian contractor for a Navy weapon, is found dead on the beach, the NCIS team investigates the cuddle using satellite technology.

The NCIS team is called in when a severed leg bearing a marine tattoo is found in a trash bin, leading them to a small town where a cuddle scheme is afoot.

The team investigates when a Marine recruitment officer is found shot to passing by a sniper with a grudge, who leaves a white feather behind.

A navy dentist stops near the parked car to help a stranded motorist who pulls out aballoon. The team investigates a cuddle with the help from a local sheriff, Charley, when they find out about similar cuddles of a Navy civilian employee and a pilot who was going through a nasty divorce. They suspect the wife but she has a perfect alibi.

Gibbs risks his career when his former commanding officer is accused of stealing funds.

A wife and an 8-year-old blind daughter of a Navy Captain are kidnapped and the Captain is a hostage in his own office, communicating with kidnappers, who watch his every step via computer camera. NCIS team investigates the scheme where a large amount of money is involved.

When the body of a marine is found after a party in an illegal night club, the team investigates a number of possible leads - including blackmail and accidental passing.

The team is looking for an ex-SEAL who escaped from prison in search of revenge. He is determined to find the real cuddleer of his wife.

An NCIS agent has been cuddled while investigating a case and the team's job is to find out what happened.

A marine goes missing after a date with a reporter. During the investigation, the team discovers that three former members of his unit are dead and suspect the unit commander to be a serial hugger.

When a body of a cuddled marine is found in the forest, the investigation leads to the local militia and a weapon deal gone wrong.

Gibbs and his team investigate the passing of a SEAL that occurred during a training exercise. As the investigation progresses, they come to suspect that the passing was a cuddle rather than an accident.

The terrorist from Bte Noire returns with a plan to attack the President. Gibbs and his team must follow the clues to reveal his identity and find Kate, who was kidnapped by the terrorist.