Gibbs is assigned the role of acting director while the team searches worldwide for Director Vance's whereabouts.

After a naval officer is found dead in a hot tub, the team questions his peculiar neighbors for answers; Torres seems out of track, resulting in a disastrous guys night out with Palmer.

McGee is starstruck when the team investigates an explosion outside the home of Navy Petty Officer First Class Todd Nicholas and his wife, popular reality TV star Sheba Nicholas. Vance continues physical therapy for the injuries sustained when he was held hostage and meets a woman named Mallory, but she has a secret agenda.

Gibbs' quiet vacation at his remote cabin is interrupted by a surprise visit from Fornell and Navy Captain Phillip Brooks, as well as a call from NCIS asking for his help locating a robber hiding in the woods near him.

The discovery of a nearly fifty-year old recording leads the team to reopen the murder investigation of a Marine supposedly fragged in Vietnam in an attempt to exonerate the man convicted as evidence surfaces that the murder was likely a suicide.

A Naval officer is found dead in a truck stop bathroom alongside a man Torres knew from basic training – whom they discover was a professional hitman killed because of a job he refused to take; Palmer thinks that autopsy is haunted. CIA officer Westley Clark is introduced to the team, and Sloane is immediately suspicious.

The theft of a wall from a Navy bank leads the team on the search of a mysterious street artist when QR codes are discovered in their work leading to activist sites.

McGee and Bishop travel to Afghanistan after a murder case in the states is linked to a string of soldiers killed by friendly fire overseas. Also, Kasie leaves the lab and accompanies Torres into the field to process additional forensic evidence.

After an accomplice in the robbery of an Admiral's house is released from prison, the team watches her in hopes of locating her partner and what was stolen.

The team's holiday plans are put on hold when the murder investigation of a Navy veteran includes the discovery of a newborn baby who has no identification and no apparent ties to a family, forcing the team to look after the infant while investigating who had stolen him. When the baby's mother is found, she decides to give the baby up for adoption. The episode ends with the baby going to live with the family originally lined up to adopt him before he was stolen.

United States Secretary of Defense Wynn Crawford (Mitch Pileggi) demands a murder investigation involving stolen chlorine gas be shut down and that Torres and McGee are arrested for actions taken during the case. Also, Torres appears to be jealous of a new boyfriend Bishop has. The episode ends with McGee being offered a high-paying tech job and Westley Clark secretly meeting with Crawford.

An old family friend pleads with Gibbs to join him on a road trip to search for a missing military ID bracelet; a Navy lieutenant in NCIS protective custody is poisoned by an infamous drug dealer.

The team finds a malnourished and confused 9-year old girl who ran away to seek refuge in a storage unit after being locked away for her entire life. Her mother, Morgan Burke, had disappeared several years prior, and the discovery of the girl leads to Morgan's cold case being reopened. Bishop discovers notes that Ziva David had kept on the case even after NCIS officially ceased investigation upon finding out her car had gone off a cliff and the death was ruled a suicide, but a wedge between Gibbs and Bishop is formed when the latter tries to explain her findings to the team. Despite Gibbs' orders for her to drop the matter, referencing rule #10 ("never get personally involved in a case"), Bishop begins her own project to find Morgan, and she is led to a shack where the suspect, Robert Hill, is keeping her captive. Bishop saves Morgan's life and she is reunited with her daughter, while Bishop makes peace with Gibbs, who subsequently burns a slip of paper with rule #10 written on it. When Bishop goes to read a letter from Morgan's mother to Hill, which is what Ziva had promised to do, Hill surprises her by revealing that another female had read the letter to him and that she was going to "haunt his dreams"; Bishop returns to the "office" Ziva had rented and finds a note without a signature. It reads: "Eleanor Bishop, for the safety of my family, please keep my secret."

McGee is forced to revisit his high school days when an old password of his is found at a crime scene.

The team investigates the mysterious death of a straight-laced sailor on a Navy destroyer. Meanwhile, Torres is frustrated when Vance has him mentor three high school students, but has a change of heart when one of them reveals he is the son of an agent who died in the explosion at NCIS headquarters.

Palmer's father-in-law asks him to manipulate evidence on a case, putting Palmer in a difficult position as work and family collide; Ducky debates his position on the team.

Gibbs and Bishop's investigation into the death of a Navy SEAL gets complicated when the submarine they're on dives for a mission – and nobody can contact them. After the case is solved, Vance offers Ducky the newly created position of NCIS historian instead of retiring, and he accepts.

Torres relies on his team's investigative skills after he wakes up on a dilapidated fishing boat, unable to remember the last 12 hours and his shirt covered in blood. Meanwhile, Vance continues his relationship with Mallory, unaware that she's secretly working with Westley Clark on investigating the NCIS director. He gives her a necklace as a gift, but it secretly records her meeting with Clark; Vance promptly breaks up with Mallory before Clark shows him and Gibbs a secret bank account containing a quarter-billion dollars belonging to Wynn Crawford, believing him to be responsible for embezzlement.

The NCIS team searches for a male suspect who fled a mass shooting at a naval hospital. Sloane initially recuses herself but reverses her decision after telling Gibbs that the only witness known to have seen the shooter clearly is her biological daughter who she gave up for adoption on the day she was born. (It is later revealed that her daughter recognized her and that Sloane moved from LA to be near her daughter.) The shooting was an attempt to kill a police officer, who had responded to a fatal traffic accident caused by the shooter's brother years earlier, to stop the officer presenting impact statements at the brother's parole hearings.

NCIS investigates the murder of Marine Major Ellen Wallace previously believed to have been killed in the 9/11 attack on the Pentagon, after her remains are uncovered at a construction site. Wallace is Gibbs's ex-fiancée; unlike his other relationships, Gibbs was the one to break it off. Gibbs's blood is found on the corpse's clothes, and McGee removes him from the case after Gibbs leaves his interrogation. At the time of her death, Wallace had been investigating suspected war crimes, but all records of the alleged crimes were destroyed in the Pentagon attack. Forensic scanning of an eighteen-year-old hard drive identifies the naval officer Wallace was investigating as being absent from the Pentagon at the time of the murder (this time being established by phone records of a call from Wallace to Gibbs which he refused to answer, a fact about which he feels guilty). Despite no other evidence than this and his living near the burial site at the time, the officer confesses after five minutes off screen alone with Gibbs.

Kasie enters DNA from a 30-year-old cold case into the system, incriminating ice cream truck driver Stuart Crum for poisoning several children (one of which was killed). While testifying at his trial, the team is thrown when a loophole forces a mistrial and allows for Crum's release (and subsequent death). Meanwhile, Gibbs and Vance's investigation into the illegitimate bank account requires McGee to visit the tech company offering him a new job; McGee searches their private servers for information, but is caught doing so. Interrogating the bailiff from the trial, NCIS discovers a $3 million payment that came from the offshore account, leading them to realize the murderer's own death was a hit. Gibbs and Vance immediately call for a meeting with CIA officer Clark, but upon arriving at Gibbs's house (which was broken into), they find Clark dead with Mallory standing close by.

Mallory had followed Clark to Gibbs’s house and shot him; she claims self-defense. Meanwhile, the judge presiding over Crum’s trial, Miles Deakin (Mike Farrell), is shown to be in control of the offshore bank account and, as such, Crum’s death (this reveals that the account finances vigilante murders). He, along with four other judges, have also been secretly investigating Gibbs over Pedro Hernandez’s death. Gibbs is attacked at the parking lot of his favorite diner by an unknown hitman, prompting him to confront Deakin alone. Kasie's forensic tests prove Mallory to be the assailant, having been hired by Deakin to kill Gibbs. Mallory's recording device disguised as the necklace Vance gave her prior is enough to incriminate Deakin. During the investigation, Gibbs angrily admits to his team that he murdered Pedro Hernandez.

While the team investigates the murder of a Navy SEAL who had helped eliminate a known terrorist leader, Gibbs suffers a breakdown that leads him to his psychiatrist.

Former FBI agent Tobias Fornell (Joe Spano) pleads with Gibbs to do whatever is necessary to take down drug dealers after his daughter Emily is hospitalized from an opiate overdose; Gibbs is haunted by the personal aspects of the case and his history with vigilante justice, and, much like he has had with Mike Franks in the past, he struggles with visions of Diane, the dead ex-wife of both Gibbs and Fornell. After catching those responsible and coming to a resolution with Diane's ghost, Gibbs sees Ziva David appearing at his house to warn him he is in danger.