Two figures break into the Portland FBI headquarters and hack the computers. When the guards spot them, the intruders use a flash-bang grenade to cover their escape and get outside... where they unmask and reveal that they're Parker and Agent McSweeten.
The next day, Parker brings McSweeten to the restaurant and tells Nate that he needs their help. Nate objects because he wants to take on a crooked financier running a Ponzi scheme, but Parker explains that McSweeten's father Peter is dying of cancer. She helped McSweeten steal some files from the FBI on the one case that Peter never solved: the disappearance of hijacker D.B. Cooper in 1971.
The team meets for the briefing but Nate still isn't in pursuing the case. Sophie, who knows about the case, informs them that Cooper hijacked a plane, demanded $200,000, and then disappeared after apparently parachuting off of the plane. Eliot believes that Cooper would have died given the weather conditions and the quality of the parachutes, and Nate figures that it's a waste of time. However, he agrees to investigate the case since he promised Parker. Hardison worries that it will take too long to go through all of the downloaded material and Parker tells him that she's gotten him some help.
FBI agent Steve Reynolds arrives at the restaurant and Hardison greets him, claiming that he and Nate are profilers working on the Cooper case. Steve was Peter's partner for years and helped him work on the Cooper case for years. The retired FBI agent explains that he always took the Cooper investigation because his wife Stephanie was a stewardess on the flight. He admits that there were dozens of theories about Cooper and what happened to him, but that none of them have ever turned out to be true.
McSweeten takes Nate to see Peter and he talks about what it's like to get into the minds of criminal. Nate admits that he has trouble taking his mind off of his work even when he's not working a case, and Peter tells him what happened in 1971.
The day before Thanksgiving, Peter (Nate) prepares to go to work for his first day as the chief of the Seattle FBI office. Joy (Sophie) gives him a new briefcase and Peter says goodbye to his son Todd before leaving. When he arrives at the Portland office, Peter thanks all of his co-workers, including Agent Wilkins (Hardison), for their hard work. He encourages them to view all cases with a sense of compassion and to remember the people that they are dealing with as people, not just cases.
On a flight heading for Seattle, stewardess Stephanie Ritter (Parker) notices one businessman watching her. He gives a note to Stephanie but she figures that he's hitting on her despite her fake engagement ring and pockets it.
Peter tells Nate that Stephanie became their main connection to Cooper as he hijacked the plane.
When Stephanie comes back to the businessman, he tells her to read the note and she discovers that it's a bomb threat because he's hijacking the plane. Cooper tells her to sit down and then shows her the bomb in his briefcase. Peter is called in and Agent Crowsley drives him to the airport. Peter and the agent on the scene, Felton, are surprised that Cooper is requesting four parachutes. Felton figures that Cooper is bluffing about the bomb but Peter isn't convinced. When the plane lands and Cooper releases all of the hostages except Stephanie, Peter decides to let him go. He figures that Cooper is bluffing about the parachutes and that he will land the plane rather than risk a mid-air jump.
While Cooper waits with Stephanie as the ground crew refuels the plane, he assures the stewardess that he's not crazy and asks her for another drink. Peter and his men arrive with the $200,00 and the parachutes and Cooper sends Stephanie to get them. Peter promises Stephanie that he'll make sure she's unharmed and leaves, and Cooper tells Stephanie to inform the pilot that he's flying to Mexico City and that he's to stay low to the ground.
At the terminal, Felton complains that Peter is making the wrong choice. Peter is sure that since the plane is flying low, Cooper is burning too much fuel and will have to land in Reno to refuel.
As the plane flies over the Cascades, the pilot gets a signal indicating that Cooper has open the aft door. Stephanie goes back and discovers that Cooper has jumped. The plane lands in Reno as expected and Peter flies there to meet with Stephanie, who gives him a detailed sketch of Cooper.
Peter explains that he was blamed for Cooper's escape because he failed to anticipate the man's actions, and that he was transferred back to the local office as a result. While he languished in obscurity, the media turned D.B. Cooper into a folk hero. Meanwhile, Hardison calls to tell Nate that he and Steve found information on a Daniel Cooper that bought a dairy farm and paid off the mortgage a year after the hijacking. Cooper was with the Army Airborne and an experienced parachutist, and Sophie goes to the farm to check him out. Nate hangs and Peter realizes that he's now as hooked on the case as he has been. When Nate suggests that Peter take a rest, Peter admits that he's never been able to rest when it came to Cooper.
Peter spends months trying to track down Cooper, letting his family life languish. On Christmas Eve he apologizes to Joy and goes back to talk to Stephanie. Before he leaves, Joy tells him that Todd is unhappy and has written up a Christmas list asking for D.B. Cooper as a present because he knows how much his father wants the hijacker.
When Peter visits Stephanie to follow up a lead on a local man claiming to be Cooper, the stewardess doesn't recognize the man from his photo. Peter admits that it's a long year and Stephanie introduces her husband, Steve (Eliot). Steve thanks Peter for his efforts on his new wife's behalf and invites the agent in for coffee. They talk and Steve explains that he's been out of work for three years since he mustered out of the Army during the Vietnam War. Peter can sympathize with how the world has changed so much for him and offers him a job with the FBI so that he can help bring Cooper to justice. Steve agrees and is soon sworn in as a FBI agent.
At the restaurant, Hardison asks Steve if he ever thought he'd end up in the FBI. Steve admits that Peter saved his life by giving him a job and that he never thought he'd survive the war.
A report comes in about some cash from the hijacking washing up on a riverbank. Peter, Steve, and Wilkins go out to investigate but Wilkins complains that it's pointless and that Cooper died years ago. Steve snaps at him and insists that he's wrong and Cooper is still alive. However, when they don't get any further leads on Cooper, the two officers are transferred to the cold-case division and start closing old crimes. In each case, Peter tries to look at the victim as well as the criminal and give both sides the benefit of the doubt.
Sophie calls from the dairy farm and informs the team that Daniel Cooper died in Vietnam in 1967, years before the hijacking. Nate calls Hardison to ask about the DNA evidence in the FBI files and the hacker admits that nothing is there. Steve figures that it's stored at the FBI crime lab and Parker breaks in to steal it while McSweeten waits in the van. Meanwhile, Nate wonders if Peter ever had any regrets about the case and the ex-agent admits that his disgrace and time away from home hurt his son Todd.
Eight years after the hijacking, Peter and Steve are at the FBI office when a witness, Michael Novak, comes in. he says that he thinks he gave the wrong description. Peter wants to talk to him but Todd calls and says that he needs help. Steve offers to interview Novak for him and Peter goes to find his son. Todd complains that some boys stole his bike, claiming that they were going to look for a lost dog. He wonders why they keep picking on him and Peter assures him that it's not a flaw to trust, and that it takes real strength to look for the good in people. Peter tells Todd that he's the best guy he knows.
Peter tells Nate that he still believes that and that he treated every person he arrested as a human being that could be redeemed. He believed that even Cooper could be redeemed. Nate admits that he has a much darker view of human nature and Peter warns that he's concerned that McSweeten could become as obsessed as he was. He tells Nate that what is important is that his son doesn't follow him into the darkness that Cooper disappeared into.
When the team meets back at the restaurant, they discover that the DNA evidence Parker stole is contaminated. Parker gets a call from McSweeten that Peter died in the night. He comes in and shares memories of Steve about Peter and how he always saw the good in people. They share a toast to Peter and McSweeten thanks the team for trying... and from now on, he plans to hunt down Cooper and bring him to justice.
When Nate studies the evidence again, Parker comes in and asks what he's doing. He explains that he wants to make sure McSweeten doesn't give in to obsession and then reviews Novak's testimony. Novak was ten years old at the time of the hijacking, but then showed up eight years later and said that he had come to believe that Cooper didn't look like the sketch that Peter showed him from Stephanie's testimony. Hardison points out that Stephanie spent much more time with the hijacker and Nate concedes that Stephanie's composite sketch is the only solid evidence they have on Cooper's identity. However, he gets an idea and has Hardison bring up the back cover of the inflight magazine on the airplane in 1971. They both realize that the sketch matches that of a man in an advertisement and that Stephanie lied.
The next day, Nate visits Steve at his home and asks about Stephanie, who died ten years ago. Steve goes to get some tea as Nate confirms that he and Stephanie married a few months after the hijacking. McSweeten comes in just as Steve draws a gun. Nate asks for the real story about D.B. Cooper and Steve admits that it's been with him since 1971.
Steve was aboard the flight as the hijacker. After the plane stopped in Seattle, he talked with Stephanie and explained that he had made a promise to provide for the family of a fellow soldier, PFC Daniel Cooper, who died in his arms in Vietnam. Stephanie admits that she's afraid for her life and that she always wanted to have a family, and Steve promises that she won't be hurt. As the plane heads to Reno, the pilot gets the signal on the aft door and Stephanie goes back to investigate. Steve is still on the plane, preparing to jump, and she begs him not to risk his life. She admits that she doesn't know whys he cares, and Steve promises that he'll see her again before jumping.
A few months later, Steve comes to visit Stephanie at her home. They kiss and soon get married. On Christmas Eve, peter visited but Steve refused to leave. After they met with the agent and had coffee, Steve wonders if Peter knows who he is and is taunting him by offering him a job with the FBI. Stephanie figures that it doesn't matter because either Peter is sincere or he's playing them, and either way they have nothing to lose. Steve agrees to take the job but his wife warns him that if he slips up then it's all over for him.
Nate explains that he had worked it out once he learned that the Daniel Cooper who owned the dairy farm served in the same unit as Steve and died in Vietnam. Steve explains that he gave most of the hijacking money to Cooper's family to pay for the dairy farm and then buried the woods in case he needed it. That was the money that eventually washed up on the riverbank. He was also in a position to contaminate the DNA evidence. Nate wonders about Novak and Steve explains that after Peter left that day, he interviewed the then-teenage boy, looked him in the eye, and convinced him that he had seen the man in Stephanie's sketch despite his doubts. McSweeten puts Steve under arrest, and the man explains that no matter what happens to him, Peter was always like a brother to him. As the agent leads Steve out, Nate asks if he really wants to put Steve in jail. McSweeten insists that's what his father wanted, but Nate points out that Peter always saw the good in people no matter how hard it was. He did eventually bring Steve to justice... by convincing him to join the FBI and help people.
Later, McSweeten goes back to his father's apartment. He finds his treasured copy of The Odyssey and the Christmas list he wrote as a boy. He then goes to the restaurant after letting Steve go. Nate tells him that he did the right thing and assures him that Peter believed that Steve deserved a second chance... and that's enough. McSweeten thanks Nate for his help and gives Nate the book, and assures Nate that he helped to end his father's long odyssey.
After McSweeten leaves, Nate asks who he reminds her of from The Odyssey. She considers him Odysseus himself, but Nate wonders if he isn't more like a siren, luring bad guys to their doom by giving them what they want and using it to destroy them. He worries that all he sees in people are their weaknesses and flaws, and Sophie points out that McSweeten wasn't that way. Nate notes that McSweeten wasn't raised by Jimmy Ford and confesses that for once, he wants to build something with his talents.