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.

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.

Someone shoots and kills the executive officer (XO) of a Naval vessel, a commander, in his own stateroom; Gibbs and company investigate. However, a shrink (a persistent and presumptuous one) arrives to conduct mandatory psychologic evaluations for all members of the gang, and she accompanies them aboard the ship. Ziva recognizes the spent brass as Russian. Word of the murder spreads fast, for seven international journalists are aboard as guests; one reporter makes a confession and reveals a potential powder keg. The team continue, and they eventually find the solution. Meanwhile, the shrink also continues, eliciting a number of flashbacks, mostly related to Kate Todd, a former member and special agent. Eventually Tony and Gibbs realize who the shrink is, then she submits her report to the director.

Gibbs and Tony follow EJ and her team to a nearly vacant building; they find that the P2P murderer has killed Levin, seriously injured Cade, and kidnapped EJ; Gibbs pursues the suspect and EJ; he finds her, left to suffocate. McGeek traces a phone number to CI-Ray (Ziva's boyfriend). Ducky, with help from Gibbs, explains the changes in the MO of the killer. From Levin's left forearm EJ secretly removes a small object. Ziva tries to intercept Ray, but Cobb, the suspect, intercepts and kidnaps her; later, while Gibbs, Tony, McGee, and EJ are present inside a hotel room, Cobb arrives, enters, and surrenders, but he refuses to tell where he put Ziva. However, Abby provides clues to a place, where the gang plus Ray find and rescue Ziva, who gives explanations. Back at the HQ, Cobb escapes with two hostages; Gibbs and others follow; a confrontation ends the career of the P2P killer. The SecNav resigns, and his successor gives Tony a highly sensitive and classified task.