Gibbs is given the task of finding a mole inside his newly formed team. With the help of Agent McGee, Gibbs is able to trace phone calls between Lee and a dead Petty Officer the team had discovered earlier. After verifying Agent Lee's logs of the calls she is cleared. Daniel Keating is focused on next and he is interrogated. During Keating's interrogation, shots are fired, and Lee is found to have shot Agent Langer, who Gibbs and Vance agree to have been the mole. At the end of the episode, McGee and Ziva rejoin Gibbs in the squad room while Agent Lee moves out and receives a text message saying, "Do they suspect?", to which she replies "NO".

Gibbs and Fornell reluctantly join forces in a murder investigation. The FBI is prosecuting a Mafia Boss. One key witness is a Marine, a man suspected to have been involved in another murder. Evidence from moldy rope used in the two murders links the crimes to the Mafia Boss. The Marine escapes from FBI protection to seek revenge, finds the Mafia Boss and shoots and kills him as Gibbs and Fornell try to stop him. Meanwhile Ziva plans for a vacation in Tel Aviv and Tony snoops around and finds a picture of a shirtless man on Ziva's desk (Ziva's partner with Mossad, although Tony doesn't know this), piquing his interest.

NCIS is targeted to investigate a series of murders by a serial killer who posts videos of the crimes on the internet. The first two victims have scrolls with links to websites of videos of their murders along with cryptic pictures spliced in. After a third video is posted, a live stream from inside NCIS, a suspect is brought in but dies in Interrogation. Video of the death ends up on the web linking the crimes to a female singer. NCIS storms a garage but Gibbs realizes that it was a setup for them to kill the singer and a man who she appears to have captive at gunpoint is the real killer. Gibbs is given a Civil Service Award but is a no-show and Tony stands in to accept the award on his behalf.

Gibbs and team are assigned a Probie to help investigate a bank robbery at Quantico. The security guard is shot and killed in the heist but only $27,000 was stolen and all of it was burned in the getaway vehicle. The Probie suggests looking into other similar cases and with DiNozzo's help finds a connection. It leads to the guard's son, a former convict, and his cell mate. Gibbs believe all parties will be at the guard's funeral, and with the Probie's help the team captures them both. Gibbs starts to believe that Agent Langer wasn't the mole in his unit and places Langer's old FBI ID at a bar wall dedicated to fallen officers and agents.

Gibbs sends DiNozzo and Ziva to try and break into a top secret military facility, telling them that it is a test of the facility's defenses. After being caught halfway through the act, it is revealed that the facility is in fact all a hoax, and that halfway through their attempt to break in, the mole set off the fire alarm and managed to gain access to the main computer, which had its keyboard laced with a radioactive substance. After returning from the operation, the director explains to the team that one of them is the mole, and explains about the radioactive trace. He scans the hands of Tony, Ziva, Gibbs, and Ducky, and then goes to scan the hands of Abby. When he does the counter ticks, and Abby is placed into custody. Subsequently, Abby is revealed (though not to Lee) to have been in on the plan to catch the mole from the beginning. The team is monitoring Agent Lee to see if she contacts anyone, believing that the team no longer suspects her. After Lee makes a mark on a newspaper dispenser, she is brought into custody. Lee reveals that she was forced to trade secrets, because her daughter had been kidnapped. They let her go, and the episode ends with Gibbs concealed in the back of Lee's car saying "Looks like we're working together".

Agent Lee becomes a reluctant participant in helping the NCIS team stop a top secret defense plan from being stolen. Lee is used as bait to capture her contact, Ted Bankston, who also tells of having a family member held captive. Bankston turns out to be the mastermind in the caper and takes Lee hostage, as Gibbs corners them on a bus. Gibbs receives minor wounds in the ensuing exchange. Lee gives a signal to shoot and is shot and killed along with Bankston. Gibbs takes Lee's badge and gives it to her "daughter" who was found alive, as the team sorts out Lee's ultimate role in the plot.

The fingerprints of a presumed dead petty officer, Ned Quinn, turn up at the scene of a double homicide. Claiming innocence, Quinn explains he was in the garage working for the victims when they were murdered. While fighting with metro police who want Quinn prosecuted immediately, the team discovers evidence linking a security guard to an emptied safe at the crime scene. Having been exposed, the guard shoots McGee with a taser and unsuccessfully tries to escape. Quinn, explaining that he went "undercover" after his apartment burnt down believing his wife and daughter would be better off with the service benefits from his presumed death, is convinced by Gibbs to rejoin his family for Christmas.

When Ducky is stabbed at a crime scene, the NCIS team must delve into his past to find clues and they uncover some disturbing secrets about his time as a doctor in Afghanistan.

While investigating the death of a Marine, the team finds Gibbs Marine ID at the crime scene. It is revealed that he helped a Colombian woman 18 years ago and that her son (whose father Gibbs killed while on the mission there) tried to contact him about a major blackmailing, involving the theft of several crates of assault rifles from a Marine base.

A Marine imprisoned for embezzlement because of a case DiNozzo was working on is released and the Navy lieutenant who witnessed against him is found dead. Tony is put in charge of the team because of Gibbs' rule #38 ("Your case, your lead") and they discover that the Marine was framed for embezzlement and now someone is trying to silence those who really did it. Gibbs' fondness of DiNozzo is shown and he announces how he is proud of his senior field agent.

Gibbs digs into Vance's past after the Director borrows Gibbs's team for an Investigation into a friend's murder. It is revealed that Tony has been in a slump with women since his break-up with Jeanne Benoit.

When shady CIA agent Trent Kort calls in a favour, Gibbs agrees to meet him at an abandoned warehouse. Upon Gibbs' arrival, he finds the agent with two dead men who claims the men shot each other before his arrival. Gibbs and the team must then work with Kort to put away one of NCIS's most wanted.

When a government scientist goes missing, Abby is recruited to carry on his work, but the team worries that she may meet the same fate as her predecessor.

The episode introduces the team of the NCIS spin-off titled NCIS: Los Angeles. Gibbs and McGee are flying to Los Angeles to work with the NCIS Office of Special Projects - Los Angeles team to solve the murder of a marine.

With the appearance of Mossad officer Michael Rivkin, Tony is forced to question Ziva’s loyalty to NCIS. Meanwhile, in Los Angeles, Special Agent Callen goes undercover to try to catch a terrorist cell while OSP psychologist Nate Getz discovers the startling truth about Gibbs and Special Agent Lara Macy’s relationship.

After a security breach at the SECNAV's residence leads to the death of an ICE agent, Gibbs and the team are forced to work with ICE and the FBI to find his killer. Meanwhile, Tony finally comes face-to-face with Michael Rivkin and after a tough brawl between the two, Tony kills him when Rivkin tries to stab him.

Ziva's homecoming to Israel with Gibbs and the team is not a happy reunion with her father, the enigmatic and powerful head of Mossad. As tensions rise, and based on information he gets from McGee and Abby, Gibbs decides to leave Ziva in Tel Aviv. Ziva is then captured by the terrorists in Somalia that Rivkin had been investigating.