Tony DiNozzo who has been working with SecNav on a special assignment has been shot and wounded even though he was wearing a bullet proof vest and is sent to the hospital. Gibbs meets with DiNozzo to tell him that he had shot another NCIS agent but Tony has no recollection of the incident or that night. While Tony recovers in the hospital, the team tries to put the pieces of the puzzle together.
In a flashback, Navy Captain Wright was killed and they find an incision on the wrist. This is the same type of incision that they had found on Levin earlier and they begin to wonder if the two are linked and if it has anything to do with Tony's secret mission. It turns out that Wright and Levin had both worked with the Office of Naval Intel on projects spying on spies and the incisions may have to do with microchips that they both may have had.
EJ, who Tony had tried to track down, confesses that she didn't have the microchip because she was delivering it to Captain Wright. Tony informs her that Wright is dead and shots are fired. Back at the lab, Abby and McGee learn that the microchips also work to open electronic doors. Gibbs and Director Vance meet Sean Latham, director of the Watcher Fleet – spies that spy on other spies). Captain Wright and Levin had worked with him before trying to prevent terrorist attacks and he needs the microchips.
Tony, EJ and Cade arrive at the meet up spot and realize that they've been set up and all of them are shot. Cade's body ends up in the river, EJ has disappeared and Tony was sent to the hospital. When he comes to he remembers that the person in the photo was Cade.
Sean Latham brings the microchips into a secret room where an auction was being held. The bids begin on the microchips. Gibbs finds a photo in Mike Frank's old files. Pictured in the group are Latham, Wright and Stratton.