NCIS season 5

Directly following the events from the previous episode, "Angel of Death", Tony is still undercover as Anthony DiNardo and meets Jeanne's father, La Grenouille, who is aware of Tony's true identity, which Tony later reveals to Jeanne, upsetting her. The team are also led to the assumption that Tony is dead, as while watching the security cameras, Tony's car explodes and Ducky's analysis indicates the body could be that of Tony, but realizes that it is not because of his lungs. Director Shepard reveals to Agent Gibbs and his team that she had given Tony an undercover mission to build a relationship with Jeanne in hopes of capturing La Grenouille after spending nearly ten years searching for him. Around the same time, Tony returns to NCIS Headquarters and is greeted first by Kort, who angrily shoves him against the wall of the elevator for worsening the situation. La Grenouille approaches Director Shepard for protection after deciding to quit the arms smuggling business against the CIA's wishes. However, Shepard refuses his plea for asylum out of pure spite and devotion to her late father. The team tries to track down La Grenouille again and find his boat, but not the man himself. They believe he made his escape and leave, but the camera pans to the water to show La Grenouille's floating corpse while also revealing that he has sustained a single gunshot wound to his forehead.

A petty officer is thought to have died in a car accident until inconsistencies at the scene indicate that the petty officer was murdered and was not the driver of the crashed car. When the car's driver is later found, Ducky conducts the autopsy and discovers that she had been beaten to death and had given birth not long beforehand, leading the team to believe that the killer has taken her child. Meanwhile, Tony tries to confront his feelings for Jeanne after her departure.

Two women find a dead Marine Captain on an Army base. One of the women is his wife, the other is Gibbs' third ex-wife. As Special Agent Gibbs and Lt. Colonel Mann conduct a joint investigation between NCIS and the Army into the murder, a DIA agent is sent to oversee Abby's handling of the Captain's laptop, which contains highly classified information. Gibbs becomes uncomfortable when he is forced into a confrontation with his girlfriend, Colonel Mann, and Director Shepard at the same time, much to the amusement of his team.

Ducky is angered when one of his research cadavers is revealed to have been a murder victim and was mistakenly tagged as a "John Doe" and donated to science. The deceased man is identified by the team as a career felon, who was working with the FBI to track down a man suspected of supplying people with new identities. They discover the man's murderer, an elusive individual known simply as "the Eraser", has ties with major terrorists organizations around Africa, Europe, and the U.S. With no face to ID "the Eraser", NCIS and the FBI join forces to find the suspect and Tony goes undercover with one of Fornell's rookie agents.

Note: Cameo appearance of the real-life NCIS Director Thomas A. Betro.

When a Navy lieutenant who worked at the Pentagon as an intelligence officer attempts to commit suicide by jumping off a rooftop, NCIS is called in to consult the officer. After Gibbs is able to persuade the officer to step down from the ledge, the officer is shot dead, falling to his death from the rooftop. Each member of Gibbs' team has a different theory on the murder, one of which includes the officer being a mole. Meanwhile, the team believes Abby is considering a job offer in the private sector.

Gibbs' team is sent to investigate a death aboard USNS Chimera, a top-secret naval research ship sailing in the middle of the ocean. After boarding the ship, they find it abandoned except for a dead U.S. Navy scientist, who died from viral hemorrhagic fever. However, they suspect that they are not alone. Their investigation is further complicated by the Navy's reluctance to share information regarding the research which took place on Chimera.

The episode begins with Tony retrieving Gibbs from the water and trying to revive him. It is revealed that Maddie, a childhood friend of Gibbs' deceased daughter Kelly, comes to him for help after being stalked which leads to the events of Gibbs' car driving into water. While unconscious, Gibbs has a vision that he is visited by his dead wife and daughter and is reassured that everything is fine.

Note: This was planned to be the 100th episode, but it was decided that Chimera was more fitting for Halloween week, so the two were switched.

Gibbs and his team investigate the assassination of a Navy admiral and meet a woman whose search for her husband, a political refugee from Africa, is related to the case. It turns out that a death squad by an African dictatorship who fear that the missing husband (who they only have a vague description of) will return to lead the opposition in the country.

While a group of boy scouts are on a visit to NCIS, Abby discovers that one of the boys was reported to have been abducted in 1998, leading the team to search for his father who is running from a murder he was accused of committing in 1998. The team launches a manhunt for the father, but are hindered by the son who warns his father in advance. During the case, Tony realizes the boy scout is a mini-DiNozzo.

The NCIS team pays a heavy price when they try to track down a Marine, Damon Werth, who believes he is still in Iraq. After a violent confrontation in which DiNozzo, McGee, and Ziva are injured, the team realizes Werth is the subject of an experiment. Things are further complicated when a Senator's aide begins interfering with the investigation, since Werth was due to be awarded a medal by the Senator and such an incident would be bad for his public image. The team suspects that the Marine was an unknowing subject of a secret super-soldier experiment, until they discover that he had been secretly taking steroids in order to qualify for the Marines. (In season 7 Werth would appear in two more episodes, "Outlaws and In-Laws" and "Jack-Knife".)

The NCIS team investigates when a Muslim Marine is found dead near a mosque that is suspected by the FBI of terrorist recruitment. But the investigation hits a snag when Ducky refuses to autopsy the Marine in deference to the Marine's family's religious beliefs as that the father believes that if Ducky cuts into his body, then his son will never find peace in Heaven. Meanwhile, the investigation leads the team to Hans Staiger, a terrorist known as "the Recruiter".

When a high-tech naval radar goes missing but is found again, the team stakes an abandoned warehouse to catch the thief – using the radar as bait. But the plan goes wrong and the radar is stolen – and a man is murdered nearby. Meanwhile, Ducky has Abby and Jimmy run some anonymous blood work, and when Gibbs finds out, he realizes Ducky is holding a secret for Jenny.

 

When the team investigates a fatal dog mauling of a suspected drug smuggler within the K-9, Abby befriends the victim's dog, names him "Jethro", and risks her career in hopes of proving the dog's innocence to save him from being put down. The team struggles with the case, with the director threatening to end it.

The discovery of the dead body of La Grenouille causes the Washington office of NCIS to be investigated by the FBI, with Jenny as the prime suspect for his murder. The NCIS building is shut down by the Bureau and Assistant Director Vance, relieving the Director and taking her place for the time. The team assembles discreetly at Gibbs' house and investigate for themselves and confirm that he was indeed murdered. After evidence comes to light exonerating Jenny, Jeanne Benoit reappears and blames Tony for the murder, at first, but Trent Kort (who has since, with the blessing of the CIA, taken over La Grenouille's business) arrives and claims responsibility. At the conclusion of the episode, Gibbs tells Jenny that the story she told wasn't accurate, and it is inferred that Jenny killed La Grenouille, due to Gibbs having seen the arms dealer putting the gun on the director's home desk although Gibbs does not take any action, simply stating, "Long live the queen".

When a Marine captain is killed during a mortar attack, it turns out that he was shot. Tony and Intel Analyst Nikki Jardine are sent to Baghdad to investigate, while the rest of the team assists by investigating stateside. The team uncovers that the man he contracted to provide soil testing hired a civilian contractor in Iraq to murder him when the captain discovers the soil sample was faked. While in Baghdad, Nikki tries to make up for a Marine mistake that led to the death of the man who helped her brother when he was wounded.

Ziva is working undercover to find a murderer who killed five women and cut off their fingers after they died, only for her cover to be blown. Before he can kill her, she manages to get into a fight with him and then shoot him with his own gun. The team is happy with the killer dead but some things are still unclear. Meanwhile, Ziva has an affair with one of the men suspected to be the accomplice of the killer.

When investigating the death of a man at a building site, Jimmy Palmer follows a suspicious man who is snooping around, only for the man to shoot at him. Left shellshocked, Jimmy struggles to remember the man's face and thus identify him. In the end, the team finds the shooter, who tries to flee, but Jimmy manages to stop him in his car.

Two boys discover a dead man, which is later identified as former NCIS Special Agent William Decker. Director Shepard attends his funeral in Los Angeles, with Tony and Ziva tagging along as protection. Agent Decker's death was ruled a heart attack, but an encounter at the funeral leads Jenny to suspect it was murder. The Director secretly brings in Mike Franks to help her investigate, believing the murder is related to a covert mission in Paris nine years ago, involving herself, Decker, and Gibbs. Devastating results follow.

In the aftermath of Jenny's death, Assistant Director Vance searches for Franks, who escaped the diner after killing the fourth gunman. Meanwhile, Tony and Ziva try to locate the one responsible, while dealing with the fallout of failing in their assignment to protect the Director. The trail points to a former hitman called Natasha, who Jenny failed to assassinate in Paris nine years previously while on an assignment that she and Gibbs were working on together. Since Gibbs killed Natasha's lover, Natasha has returned to the U.S. seeking revenge. Natasha, who never saw it coming, is killed by Franks, after Gibbs set a trap for her at Jenny's house. Gibbs burns down the house to cover up Jenny's death, making the public believe she died of smoke inhalation. In the fallout of Jenny's funeral, newly appointed Director Vance shreds a page from his personnel file in the Director's office and terminates Ziva's liaison status (sending her back to Israel), reassigns McGee to the cyber crime division, and sends Tony to the USS Ronald Reagan. Vance then gives Gibbs personnel files for his new team members.