At the Portland FBI headquarters, two figures break in and hack the computers. They download the files just as two guards come in, interrupting them. The intruders use a flash-bang grenade. As they leave, Parker and McSweeten remove their masks.
The next day, Parker brings McSweeten to the bar. Nate objects because he's busy looking into Oliver Schmidt's and his Ponzi scheme. However, Parker explains that McSweeten's father is dying and that she helped him break into FBI headquarter to steal files on an old case. Nate agrees to talk to him and McSweeten explains that his father has one unsolved case that he wants to finish before he dies: finding D.B. Cooper.
The team meets and Nate insists that the job is just a detour. Sophie relates the case of how D.B. Cooper hijacked a plane in 1971 and then jumped out over the Cascades when he got the $200,000. He has never been seen since. Eliot points out that he was in a 1971 parachute and jumped out in bad weather, and figures that he didn't survive. Nate says that it's a waste of time but agrees to keep promise to solve it. When Alec points out it will take forever to go through the files, Parker says she got him some help.
FBI agent Steve Reynolds arrives to meet with Alec and Nate, who are posing as FBI consultants. Reynolds partnered with Peter McSweeten on the Cooper case. Reynolds says that the case was personal because his late wife was a stewardess on the plane. He tells them that Richard McCoy hijacked a plane a year later, was sent to prison, escaped, and died in a gunfight with the FBI. Another man in 1995 admitted to being Cooper before dying. He figures that there are hundreds of theories.
McSweeten checks on his father and brings Nate along. They talk about what it's like to get into the mind of criminals and Nate admits that he can't leave it at the office. Peter begins telling his story of what happened in 1971.
The day before Thanksgiving, Peter (Nate) dresses for his first day as chief of the Seattle office. His wife Joy (Sophie) gives him a new briefcase. He stops by Portland division to thank his co-workers (including Agent Wilkins--Alec) and praises them, telling them to put themselves in the shoes of the people they serve.
On a 727 flight to Seattle, the stewardess Stephanie Ritter (Parker) welcomes one of the passengers, a businessman. He gives her a note and Stephanie pockets it.
Peter explains that Stephanie became their connection to Cooper.
Cooper tells Stephanie to read the note and she discovers that it's an explanation that they're being hijacked. She sits down with him and Cooper shows him the bomb. Peter and Agent Crowsley go to the airport once they receive word of the hijacking. Among Cooper's requests are $200,000 and four parachutes. When they arrive at the FBI office, Felton explains his plan to take out the hijacker once the plane touches down. He figures that the bomb is a fake and that they're in no danger, and asks Peter what his plan is. When the plane lands, they discover that the shades are down. Nate tells the agents to give Peter what he wants once he releases the hostages. He figures that the parachutes are a bluff and Cooper will land the plane
On the plane, Cooper lets everyone go but Stephanie. He assures her that he's not crazy and asks for another drink. There's a knock at the door and Cooper sends Stephanie to open it. It's Peter with the money and the parachutes. He promises Stephanie that he'll get her out safe and leaves. Cooper then tells Stephanie to order the pilot to fly to Mexico City and to stay low.
Back at the terminal, Felton complains that they're letting Cooper go. Peter figures that Cooper is having the plane fly low and that he will have to land at Reno because he's burning too much fuel.
In the cockpit, the pilot informs Stephanie that the aft door has just been opened. She runs back and discovers that Cooper has jumped. When the plane lands at Reno, Peter gets Stephanie to provide a sketch of Cooper.
Peter tells Nate that he was transferred back to Portland as part of an unofficial demotion.
Peter returns to his office while the radio plays songs about the newest folk hero, D.B. Cooper.
Nate gets a call from Alec and Reynolds about how a Daniel Cooper bought a farm and paid off the mortgage in 1972. Cooper with a parachutist with Airborne and Sophie is heading there. When Nate hangs up, Peter realizes that he's obsessed. Nate laughingly passes it off and asks if they want to take a break, but Peter says that he never rests when it comes to Cooper.
Peter continues trying to find Cooper, obsessed with the hijacker. On Christmas Eve he's still following up leads and apologetically tells Joy that he has to stop Cooper so that he doesn't inspire more hijackers. She tells him that Todd has Cooper on his Christmas list and figures that his father wants the hijacker more than anything else in the world.
The agent goes to see Stephanie and shows her a photo of a man who is going to bars claiming to be Cooper. Stephanie doesn't recognize him and Peter admits that it's been a long year. As he starts to go, Stephanie's husband Reynolds (Eliot) comes out and thanks Peter for his efforts, and asks him never to give up. Peter decides to accept some coffee and they go in and chat. Reynolds explains that he hasn't been working in the last three years since the Army sent him home. He admits that it feels like the world has turned upside down, and Peter sympathizes. He offers Reynolds a job to help him bring Cooper to justice. Reynolds is soon sworn in as a FBI agent
Alec asks Reynolds if he ever thought he'd end up in the FBI. Reynolds says that he never thought he'd live so long after making it through the war, and that Peter saved his life by giving him a job.
Peter, Reynolds, and Wilkins are called in when cash from the Cooper ransom washes up on a riverbank. Wilkins doesn't see the point, figuring that Cooper died a long time ago. Reynolds loses his temper and then tells Peter that Wilkins is wrong. After that, Wilkins and Reynolds took over the cold-case unit, solving crimes.
Sophie calls to tell Nate that the Daniel Cooper she was sent to find died in Vietnam in 1968, three years before the hijacking. Nate then calls Alec, who tells him that there's no DNA evidence in the files. Reynolds figures that it's stored in the crime lab. Parker breaks in and recovers the information, and brings it out to McSweeten kin the van.
Nate asks if Peter had any regrets about the case, and the agent admits that it was hard on his son Todd.
One of the witnesses from the plane, Michael Novak, comes in to the FBI office because he's afraid he got the description wrong. Peter is eager to talk to him, but he gets a call from Todd. Reynolds tells him that he has the interview and Peter goes to find his son. Todd explains that some kids stole his bike and that they keep picking on him, and wonders why it keeps happening to him. Peter says that it's easy to see the bad in people but tells Todd that it's not a flaw to trust. He tells his son that he's the best guy that he knows.
Peter insists that everyone that he arrested was a human being and that he believed they could be redeemed, even Cooper. Nate admits that he doesn't believe it and Peter explains that he's worried that Todd will become obsessed trying to avenge his loss. He says that finding Cooper isn't important: what is important is making sure McSweeten doesn't follow him into the darkness.
Back at the restaurant, the team discovers that the DNA evidence was contaminated and useless. Parker gets a call from McSweeten informing them that Peter has died. He comes in and talks with Reynolds about their memories of Peter. Reynolds describes an incident when Peter believed a strung-out girl and found a killer, and offers a toast to his partner. McSweeten thanks them for trying and says that from now on, he'll be hunting Cooper.
Nate goes back to study the evidence and Parker asks what he's doing. He refuses to let McSweeten become obsessed with Cooper and goes back to Novak's testimony. Novak was ten at the time of the hijacking and remembered eight years later that Cooper didn't look like the sketch. Alec figures that Stephanie's description was more accurate and that she was seated next to him for hours. When Nate points out that the only solid piece of evidence they have is Stephanie's description, he gets an idea and asks what the inflight magazine was on the flight. Alec brings it up and they realize that Stephanie's description matches the photo on the back cover advertisement.
The next day, Nate goes to see Reynolds and asks about Stephanie. Reynolds explains that Stephanie has been dead for ten years and goes to make some tea. Nate confirms that they were married in 1972 and Reynolds draws a gun... just as McSweeten comes in. Nate asks for the real story of Cooper and Reynolds admits that he's been carrying it around with him for a long time.
Reynolds was on the flight and gave Stephanie the note. As they sat together waiting at the Seattle airport, Reynolds reveals who he is and explains that he made a promise to PFC Daniel Cooper, a dying solider. He promised that he would take care of Cooper's family. Stephanie explains that the engagement ring she's wearing is just to keep drunks away but she wants to have a family. Reynolds assures her that he won't hurt her. Later, the plane takes off for Reno and Stephanie goes back and sees Reynolds about to jump. She says that it doesn't matter who died and begs him not to jump. When Reynolds wonders why she cares, Stephanie admits that she doesn't know and Reynolds promises that he'll see her again. He jumps and Stephanie looks on, screaming.
Later, Reynolds comes to Stephanie's home. They greet each other and kiss. Once they're married, they're at home on Christmas Eve when Peter comes over. Reynolds refuses to leave and tells her to answer the door. Once Peter leaves, Reynolds says that he wanted to see Peter and figures that he's taunting him by offering him a job. Stephanie believes that Peter doesn't know that Reynolds is the hijacker and suggests that Reynolds accept his offer because they have nothing left to lose. He agrees but Stephanie warns him that if he slips up even once then it's all over.
Nate realizes that Cooper died in 1968 in Vietnam and that he served with Reynolds. Reynolds explains that he used the money to buy the dairy farm for the Cooper family and buried the rest, and admits that he contaminated the DNA evidence. Nate wonders about Novak and wonders how Reynolds fooled the boy, and Reynolds explains that he just looked him dead in the eye and lied. When he interviewed Novak the second time, he looked him in the eye and bluffed. McSweeten arrests Reynolds, who says that Peter was like a brother to him and nothing will ever change that.
As Reynolds is taken away, Nate approaches McSweeten and asks if he really wants to put Reynolds in jail. McSweeten insists that his dad wanted Cooper in jail, but Nate points out that Peter could see goodness in people and that he did bring people to justice... by convincing Reynolds to become an FBI agent.
Later, McSweeten goes back to his father's apartment and puts his old briefcase on his father's chair. He finds his old Christmas list, crosses himself, and then goes to the restaurant. Nate tells him that he did the right thing and McSweeten wonders if Peter knew. All Nate can say is that Peter figured that Reynolds deserved a second chance and says that's enough. McSweeten thanks him and gives him his father's treasured copy of Homer's The Odyssey
. He assures Nate that he was the one who ended his father's odyssey and walks away.
Sophie comes in and Nate asks her who she would choose from the book that represents him. She says that Odysseus is the hero that reminds her of Nate, but he describes himself as a siren. Nate says that his talent was originally to see what they could do together, but now he offers people their deepest desire to destroy them. He worries that all he sees are flaws and weaknesses because that's what he looks for. When Sophie points out that McSweeten wasn't that way, Nate says that McSweeten wasn't Jimmy Ford's son and says that he wants to build something.