A body is discovered in the water system on a Marine Base. A note stuffed inside the victim's mouth leads to a website showing how the first victim was killed. The team races to find the culprit because they know there will be more victims.
Gunmen rob the credit union at Quantico and kill a guard; Gibbs and company investigate; they question whether getting cash was the objective of the robbers. The team make several connections, then they round up the bad guys at a burial.
After an elaborate setup Tony and Ziva break into a classified Navy facility; however, that test is itself a ruse by which to identify a mole within the NCIS. Gibbs and Lee meet in the chat room, and Gibbs says that now they work together.
Tony and McGee unsuccessfully try to follow Lee's pickup man; a satellite leads the gang to a house with a secret room and a dead body; a second stakeout produces a different result, which takes the team to a solution, a catch, and more.
A boatswain's mate dies after a single-car crash; Gibbs and company find evidence of gunfire plus beatings of the victim, who was a member of a fight club and, they learn, the operator of an illicit business. The gang figure out all of it.
A Metro detective investigates a burglary and double homicide at Christmas in Washington; the suspect is a former Navy petty officer who supposedly died 17 years ago; the Gibbs gang take an interest, find the pieces, and put them together.
An old skeleton comes to light; Gibbs sends McGee to question a prisoner convicted of murder in two identical cases; while he does so, other inmates kill a guard, seize McGee, and take over. McGee successfully negotiates and investigates.
On a sidewalk a former fiancée fatally stabs a petty officer; while Gibbs and company investigate, a different woman accuses Ducky of a war crime and stabs him through one hand. Ducky surrenders, but Gibbs sorts it out and gets Ducky free.
Two kids find the disemboweled body of a missing Navy captain; Gibbs and company investigate; Ducky finds a pentagram impressed into the victim's back. Another man dies. The team put the pieces together, and Gibbs and Tony nab the bad guy.
The Metro PD finds the body of an 18-young-old Marine who had grown up in the same hood where he died; the Gibbs team investigate with the help of Franks. They slowly assemble the picture, then a gentle social worker offers the last piece.
A man, impersonating Tony, dumps the body of a witness against him in a trial during which the impostor became convicted and imprisoned as a result of one of Tony's investigations; Tony and the gang sort out some of it but not all of it.
An agent of the NCIS dies in an execution-style shooting; Gibbs and company investigate. A radioactive painting provides clues, and an impostor federal agent causes trouble, but Gibbs and Tony, on horseback, and the others break the case.
Vance, using members of the Gibbs team, in Chicago works the case of the murder of a man who, Vance insists, was once a member of the Marine Corps. Gibbs wonders whether Vance has exceeded his authority. Later Vance hears what happened.
In Navy base housing in Norfolk, Virginia, a mother finds a pistol among the personal stuff of her 12-year-old son; Gibbs and company find a trail of old crimes and two recent deaths. The gang put the pieces together and find the shooters.
Kort dishonestly gets help from Gibbs and his team in neutralizing an international mobster who "has returned to the US". The bad guy's CPA, who launders his dirty money, enters the picture. Deaths abound, and the gang figure it out.
Local cops find the body of an enlisted Marine on UA; Gibbs and company investigate. The FBI haul Abby to a classified lab to replace a missing man, who was a target of the dead Marine. The gang figure it out and tie up the loose ends.
Gibbs and company start looking into the murder of a Marine. Gibbs and McGee go to Los Angeles for a joint gig with the NCIS Office of Special Projects in LA due to a suspected link. The investigation continues on both coasts. [Continued.]
Gibbs and McGee continue with the OSP in LA. Rifkin shows up and interferes with the NCIS investigation. Two sleepers in a terrorist cell die, but OSP agents swarm a shop and grab others. Gibbs intercepts Rifkin and tells him to go home.
During a poker game at the home of the SecNav, an ICE agent dies while on the protection detail; Gibbs and company investigate with support from the FBI and ICE. An invisible man becomes visible and dead. Tony arrests Michael, who resists.
Ziva finds Tony and Michael on a floor; Michael dies soon afterward; the next morning her pad explodes. McGee and Abby find answers. Vance, Gibbs, Tony, and Ziva go to Tel Aviv; Ziva remains, and the others return; Ziva runs into trouble.