John Cooper, a prisoner, has been transferred to a medical clinic for dialysis because he’s missing a kidney. The nurse, Nancy, says that she’ll see him next week. As the guard takes Cooper out, he complains that the prisoner is getting preferential treatment over his mother, who is on a waiting list. As they arrive at the van, Cooper uses a paralytic vial hidden in his bandages to knock one guard out, take his gun, and tell the complaining guard to close the door and let him go.
At home, Michael is on the Internet watching videos of the player that Rex will be playing in his tennis tournament that weekend. Rex comes in with Tara and complains that he doesn’t want Michael watching him lose, because he’ll be going up against a ranking player. Before he can respond, Michael gets a call from Bird, who tells him that Cooper has escaped. Michael remembers that he was the one who put Cooper away after the man shot a drug dealer, Derek Bell, who got Cooper’s son hooked on drugs and ultimately killed. The detective apologizes to Rex for missing his game, but Rex is relieved that Michael won’t be there.
At the station, Michael discovers that his ex-partner, Jim Mayhew, is waiting for him. Mayhew wants in on the case, since he helped put Cooper away. They go into the squad room and Michael is surprised to learn that Mayhew and Bird know each other, until they admit that they met at Hannah’s funeral.
When Michael comes home from jogging, Hannah reminds him that David Wilson from the counseling clinic called to remind them that they’re holding a fundraiser in Rex’s honor, since he had volunteered there. Michael reminds his wife that they had decided not to go, but she thinks that they should be there, even though it will be hard for her.
Lee asks Michael if he doesn’t want to go to the memorial service because he’s concerned about accepting Rex’s death and losing his dreams, rather than to protect Hannah from grief.
As they drive to the tournament, Tara asks Rex why he doesn’t want his father there, and the teenager admits that he’s uncomfortable around Michael because he wishes that Hannah had survived the crash rather than his father. The coach assures him that he’s not a terrible person and that what he needs to do is talk it out. A car rear-ends them and Tara goes to talk to the driver. It’s Cooper, who knocks her out with the paralytic. Rex sees the convict coming and manages to hide Tara’s cell phone in his sock before Cooper breaks in the car window and grabs him.
Michael gets to the crime scene and starts badgering Tara for details, insisting that Cooper must have told her. Bird pulls his partner away and Mayhew confirms that Rex has Tara’s cell phone. Michael figures that Cooper must want to bargain since he captured Rex rather than killed him immediately. Bird gets a report that the dialysis nurse, Nancy, failed a field polygraph test and Michael goes to interrogate her.
Rex wakes up inside of a shed, handcuffed to the floor. He tries to dial 911 on the cell phone but Cooper comes in, interrupting him. When Rex warns him that his father is a cop, Cooper ignores him and the teenager starts screaming for help.
Michael talks to Nancy, who admits that she helped Cooper escape but didn’t know he would abduct anyone. However, she has no idea where Cooper might be and explains that he doesn’t have anyone else. As Michael leaves, Nancy asks him to forgive her and says that she’ll pray for Rex’s safe return. Outside, Bird tells Michael that Mayhew is coordinating the canvass of the neighborhood and that Tara is there to see him. Michael goes to his desk and Tara tells him that Cooper called and left a message with a phone number to call. When Michael has the number traced, he discovers that it belongs to a payphone outside the station. He draws his gun and runs outside, and spots a black man in Cooper’s hoodie. The detective advances on the man and confirms that it’s not Cooper. The man admits that Cooper paid him $40 to stand there. The payphone rings and Michael answers it. Rex is on the other line and starts to yell for help, but Cooper gags him and then gives Michael a time and an address in San Bernadino. He tells the detective to come alone and hangs up. Cooper then apologizes to Rex, saying that no son should pay for the sins of the fathers, and walks out of the shack.
Michael goes to the warehouse at the address and finds Cooper waiting for him. Cooper doesn’t put up a fight, but warns Michael that he’s the only one who can lead the detective to his son, and that Rex will soon die of exposure. He insists that he wants justice and that someone else killed Bell and framed him. Cooper explains that after ten years he’s finally figured out who killed the drug dealer and wants Michael’s help to approve it. Before he can say anything more about Rex, Bird and Mayhew arrive with a SWAT team, and they shoot Cooper before he can talk. Michael begs the dying Cooper to tell him where Rex is, but the man dies without saying anything. Disgusted and angry, Michael tells the two officers that they just killed his son.
Michael goes outside and Bird explains that he followed him since the captain figured that Cooper would call Michael. When Michael points out that Cooper claimed he was innocent, Bird doesn’t believe it and tells Michael to clear his head if he wants to find Rex. Michael gets an idea, goes home, and take some sleeping pills.
Hannah comes out of the shower, waking Michael. The detective calls Vega and has him confirm that Cooper in this reality is still in prison. Vega wonders why and Michael says that he should trust him because he’s his partner, and then takes the day off. As he dresses, Hannah comes in and reminds him about the fundraiser. Racing to save his son in the other reality, Michael lies and says that Vega called him in to find an abducted boy that is Rex’s age. Angry, Hannah tells Michael to let someone else take the case so that he can be there to honor his son at the fundraiser, but he insists that he can’t and his wife walks away.
At the Metro Youth Center, Hannah gets up in front of the audience and talks about how Rex was a reluctant volunteer at first since it was a community service requirement. However, he soon spent extra hours there, and Hannah once came in and listened in secret as Rex talked a young girl, intent on hurting herself, into getting help. Crying, Hannah talks about how she hugged Rex and will always have the gift of knowing who her son really was and what he might have become.
As Michael arrives at the prison, he calls to apologize to Hannah and leaves a message saying that he’s doing the best he can.
Using Tara’s cell phone, Rex records a message for anyone who finds it, asking them to get it to his father.
Michael meets with Cooper and claims that he’s received an anonymous call saying there’s evidence that Cooper is innocent. The detective says that he wants to make things right and Cooper points out that he can’t give him back the last ten years of his life in prison. When Michael asks if he knows about a shack in the desert, Cooper figures that something is up and wonders how it can prove his innocence. He accuses Michael of reusing to consider that he might have been innocent because then he’d have to admit that he screwed up ten years ago. Cooper offers the information in return for Michael getting him out, and Michael seriously considers that Cooper might be innocent. He asks who the convict thinks did kill Bell, and Cooper says that he used to think it was Michael, because it had to be a cop who had control of the evidence.
Michael leaves the prison and calls Mayhew, and offers to come over for a beer. However, once Michael comes over, he reminds Mayhew that Bell had a million dollars but only $100,000 ever turned up. He figures that Mayhew killed Bell, took the money, and planted the gun in Cooper’s house. When Michael demands his share of the stolen money, Mayhew says that there is no money. He’s unaware that Vega and a surveillance team are outside, listening in. Mayhew says that he knows that Michael has been having psychiatric problems and figures that the belief that Mayhew took the money is a delusion. Michael threatens to go to IA and have Mayhew’s bank records subpoenaed, but Mayhew still insists he doesn’t have the money. However, as Michael starts to walk out the door, Mayhew finally cracks and admits that he took the money and spent most of it, but that Michael can take what left. Michael walks out without a word, and when Mayhew goes after him he discovers that the police are at his doorstep, ready to arrest him. Meanwhile, Vega admits to Michael that he wasn’t sure if his partner had dreamed up the entire thing. Michael admits that he wasn’t sure if he had either, and calls the prison warden about Cooper.
Once he wakes up and has the shack’s location, Michael takes Bird and a team of EMTs to the shack. Bird wonders how Michael put it together, and wonders if it’s connected to Mayhew being arrested for Bell’s shooting after a check of his bank accounts. He figures that Cooper must have been innocent and Michael agrees with him. They arrive at the shack and find Rex weak from dehydration but alive and well. Michael hugs his unconscious son and cries as the EMTs go to work.
Lee figures that Michael always subconsciously believed that cooper was alive, and that the man’s recent failed appeal triggered Michael’s dreams about the man escaping and abducting Rex. Michael doesn’t believe it and insists that he would never have buried the idea if he thought something was wrong. However, Lee figures that the dream was merely a reckoning for Michael’s conscience.
Dr. Evans suggests that Michael blamed himself for sending Cooper to prison and that he tried to alleviate his guilt by creating a dream-reality where he freed Cooper. When Michael points out that he doesn’t feel any better, Evans wonders where his inability to forgive himself comes from.
Michael goes to the hospital to see Michael, and Tara comes in. He assures her that his son will be going home the next day and tells her not to blame herself. Tara gives him her cell phone and explains that Rex recorded a message on it or his father. She says that Michael needs to hear what his son had to say. The detective plays back the recording and listens as Rex says that he doesn’t blame Michael for what happened to Hannah.
When Michael looks up the next day, he looks at Rex’s memorial brochure. Hannah asks if he found the teenager that he said was abducted and Michael tells her that they did and that he’ll be okay. He tells Hannah that he thought about her all day and wanted to be at the service with her, and apologizes because he couldn’t. Hannah takes his hand and admits that it was hard, and wishes that Michael had been there so he could feel the love for their son.
On the recording, Rex says that he loves Michael and will hold onto that love until he sees him again.