Season 2

The wife and nine-year-old blind daughter of a Navy captain are kidnapped and the captain is a hostage in his own office, communicating with the kidnapper, who watches his every step via computer camera.

A mummified remains of a woman are found in an abandoned compound. The team discovers that the woman was missing for several months, was wearing a wedding dress when she died, and might have been a victim of a serial killer.

The NCIS team is called in to investigate when a perfectly functioning Marine helicopter is found in the middle of a crop circle.

A body of a woman in a Navy uniform is found by two sailors. Ducky links the murder to an unsolved case from ten years ago, and the team searches for a serial killer who left a note promising to return.

NCIS discovers that an area in a Marine's bombing range is where mafia has been dumping bodies for a while. One of the victims is an undercover FBI agent. The team sets out to find a mole.

The team must protect an Iraq veteran due to the threats made by terrorists. While trying to convince FBI Agent Lina Reyes to help them, the team is convinced that they have discovered the bomber.

Ernie Yost, an elder Marine veteran confesses to murdering his best friend almost 60 years ago in a war battle. The NCIS's job is to solve the secrets and save Ernie from prison.

A strange case for Gibbs and his team opens when a Navy Commander dies after successful surgery. While researching the commander's past, the team finds out that he collected a lot of enemies lately.

Laura Rowen, a Marine's wife, shoots an intruder in self defense when he is about to rape her. The team takes on the case and finds out that the wife is leading a double life while her husband is serving overseas.

Tony disappears while doing an undercover operation as an escaped prisoner who is forced to stick to a convict that owns a key to an expensive ancient Iraqi sculpture. The GPS locator that Abby planted on Tony stops working and the team is forced to find Tony before he gets murdered by the thief.

A dead body of a two-year-missing Navy officer appears on the bottom of a lake. The team investigates the case with a help of a private detective.

The team takes on another strange case when a telemarketer reports a possible murder of a Petty Officer who appeared to be dying over the phone.

A "meat puzzle" starts when Ducky identifies the pieces of three bodies that were stuffed inside a barrel a few months ago. They turn out to be bodies of a judge, prosecutor, and jury foreman that worked with Ducky on a rape case ten years ago.

Erin Kendall claims to have seen a murder of a sailor in an apartment across from hers. Gibbs assigns the case to McGee who believes that he can resolve it himself. However, due to the lack of physical evidence, McGee turns to the team to help him.

The team takes on a case of a dead Marine who recorded his death while falling off a cliff. The prime suspects are his wife and his best friend with whom he had a picnic in the camp. Gibbs finds out they had an affair behind the dead man's back.

NCIS starts an investigation after Petty Officer Manda King is found dead in a bartender's bed. The suspect is the owner of a competing club where Manda's sister sings.

When a sailor officer receives a pair of blue eyeballs, the NCIS team starts investigating the case. Gibbs traces an ex-Navy agent that does illegal work.

A Petty Officer that just returned to her job is found dead in the backstage of a bikini contest. The team finds out that she possibly had a stalker behind her back.

The team investigates a suicide case, believing that the main reason of her death is a nervous breakdown, but Ducky believes that she was actually murdered. FBI Special Agent Fornell helps them in the investigation. The team discovers that the dead woman was involved in a love triangle and that this may have contributed to her death.

After a Marine is murdered in a school campus the team discovers a possible suspect for his murder, but they soon find the suspect murdered. Tim and Abby discover a trace to a "Red Cell" in the e-mails and the team believes that maybe the Marine was involved in a serious game.

A young Marine is killed in Iraq, but he was investigated by police for a murder on a young girl in his hometown. While going through his personal belongings, they find the body of that girl. The local police believes that the corpsman murdered the girl, but Gibbs believes that he is innocent and he will try to prove it with a help of Faith Coleman.

When Tony opens a mysterious letter thinking it's for him, a small puff of white powder comes out and releases a possible deadly virus. Soon Kate and Tony are isolated in a bio-hazard isolation room for precaution. McGee and Gibbs work to discover who sent the envelope and how to cure their friends before it's too late for them.

A group of serial terrorists seek revenge and send Ari on an assignment to kill Gibbs. The NCIS team goes on a hunt after him, but when they discover that Ari has a bigger plan, it is already too late.