The FBI tells Gibbs (MARK HARMON) that his former commanding officer, Colonel Ryan, has gone AWOL. Having recently been spotted in an airport – fleeing to the U.S. after a stint in Iraq -- Ryan is suspected of having staged an incident, killing a marine and then absconding with millions of Hussein’s found money. However, Gibbs is certain Ryan could never be guilty of that; he enlists Kate (SASHA ALEXANDER) and Tony (MICHAEL WEATHERLY) to try and find Ryan which takes them to the Colonel’s hideaway cabin. While there, the agents find that the place has been splayed with bullets and find a dead, unidentified man. Gibbs unfortunately also spots a bomb and the agents barely escape as the explosion rips through the cabin, destroying any evidence of Ryan’s whereabouts, and charring the victim inside.
As Ducky (DAVID McCALLUM) tries to determine the victim’s identity, Gibbs gets a call from Ryan, who wants to meet with him... and shrugs off any possibility of having Gibbs bring him in. Ryan relays that he is convinced that a conspiracy at high levels is at work. And, almost in proving his point, Gibbs has to elude FBI agents who are following him on his way to meet Ryan. When he does, Gibbs finds his former C.O. injured. Upon Gibbs’ questioning him about the man killed inside his cabin, Ryan insists he was trying to find out who the man was and is certain he is part of the conspiracy. He produces a videotape that he claims will prove his innocence in the killing; the tape was recording the activities inside the cabin, but it is shredded in parts. Still, Gibbs says he will help Ryan.
Then, FBI agents, including lead FBI Agent Fornell, arrive at NCIS headquarters to interrogate Gibbs about his meeting with Ryan. At that time, Gibbs realizes that the unidentified victim is actually an FBI agent who had been tailing Ryan. Further, the FBI had only involved Gibbs because they knew that Ryan would try to seek him out. Worse, at this point, Ryan is suspected of both embezzling the money and murdering the FBI agent.
At Gibbs’ home, Ryan shows up again, as the agent tries to talk him into coming into NCIS. Still Ryan is convinced of evil forces at work at the top-tiers of the government.
Ryan also divulges that he is working with a Captain Cameron, but that assertion troubles Gibbs. Cameron was Gibbs’ company commander and died in his arms... with Ryan standing right there when it happened. But Gibbs’ persistence about Cameron’s death only fuels Ryan’s conspiracy theory that much more; Ryan insists that Cameron is alive, and that they saw and believed “what they wanted us to see.”
With that, Gibbs agrees to follow Ryan to another hideout, a warehouse where some money is hidden that will help fund his resistance against the conspiracy. When Gibbs calls Tony from the warehouse, the FBI traces the call and descends upon the warehouse. In the meantime, Abby (PAULEY PERRETTE) has been able to grab an image from Ryan’s corrupted tape that identifies a man on the scene as reserve Army Colonel Mike Granger, who rotated out of Iraq just two weeks ago. Kate realizes that Granger is not only the culprit in taking millions more of Hussein’s found money... but also killed the FBI agent at Ryan’s cabin. Kate finds a current work address for Granger and relays it to Gibbs, who reveals the information to Ryan.
As Gibbs and Ryan are seemingly cornered by the FBI, Ryan manages an escape. While the FBI now want to take Gibbs in, he talks FBI Agent Fornell into going with him to track down Ryan, who has headed to Granger’s office. When Gibbs and Fornell arrive there, Ryan has drawn a gun on Granger and is threatening to fire as the reserve Colonel admits to taking found money in Iraq as payment for risking his life. At the same time, Ryan is communicating with Cameron – whom Gibbs now knows is just a figment of Ryan’s schizophrenic imagination. Explaining to Gibbs how Cameron bled out in his arms, he is finally able to bring Ryan back into reality. With truly no conspiracy being played out, Ryan had allowed his time served – and Cameron’s death -- to take its toll on his mental faculties, and had become a paranoid schizophrenic. With Gibbs’ belief in his former C.O., Ryan will now get the help he needs and deserves.