Season 2

A wife and a 9-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 large amount of money is involved.

A mummified remains of a woman are found in the abandoned compound. The team discovers that the woman was missing for several months, was wearing a wedding dress when she died, and might've been a victim of a serial killer. The search for the murderer leads them to Florida, where they start looking for another woman who mysteriously disappeared after going to work. One of the clues they have is the old manual for good wifes.

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 the Navy uniform is found by two sailors. Ducky links the murder to an unsolved case from 10 years ago, and the team is searching for the serial killer who leaves the note promising to return.

NCIS discovers that an area in the Marine's bombing range is where mafia has been dumping the 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 the terrorists. While trying to convince an FBI Agent Lina Reyes to help them, the team is convinced that they have discovered the bomber. However, more secrets are about to be revealed...

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

A strange case for Gibbs and his team opens when a Navy Commendar dies after successful surgery. While researching through commander's past, the team finds out that he collected a lot of enemies lately and tracks down a ensign making him the prime suspect. Soon Abby realizes that they got the wrong man...

Laura Rowen (guest star Megan Ward), a Marine's wife, shoots an intruder in self defense when he is about to rape her. The team takes upon the case and finds out that the wife is leading a double life while her husband is serving overseas. Allegedly, she has been chatting with a stranger on the net and had no idea about his true intentions. The team believes that she might have lured him to her home, not knowing that he is a serial rapist...

Tony disappears while doing an undercover operation as an escaped prisoner who is forced to stick to a convinct 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 2-year-missing Navy officer appears on the bottom of a lake. The team investigates the case with a help of a private detective. Meanwhile, a famous family offers a lot of money in exchange for the information about the missing body. The team is surprised when a bullet is found in a car. Now the dissapereance becomes a murder...

The team takes upon another strange case when a telemarketer reports a possible murder of a petty officer who appeared to be dying over the phone. However, with the help of Virginia officials, the team finds out that officer's call was just a big joke using the computer skills, until he is actually found dead...

A "meat puzzle" starts when Ducky identifies the pieces of three bodies that were stuffed inside a barrel few months ago and they turn out to be bodies of a judge, prosecutor and jury foreman that worked with Ducky on a rape case 10 years ago. Gibbs believes that Ducky might be the next victim of the killer, so he orders the team to keep him and his mother safe. Even so, Ducky is kidnapped during the investigation and now the team must find him before it's too late.

Erin Kendall (guest star Danica McKellar) 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 and he tries to persuade each of them to blame each other. Meanwhile, Abby reconstructs the case using her computer skills to handler the Marine's camera...

NCIS starts the investigation after petty officer Manda King is found dead in the bartender's bed. The suspect is the owner of the 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 comes on a trace for a past Navy agent that does illegal work.

A petty officer that just returned to his job is found dead in the backstage of the 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 the school campus the team discovers a possible suspect for his murder, but they are soon leaded back to zero point when they find the suspect murdered. Tim & 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 (guest star Alicia Coppola).

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

A group of serial terrorists seek revenge and send Ari (guest star Rudolf Martin) 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... the NCIS team will have to face the death of one of their team members...