In Walnut Creek, California, an innocuous-looking man seemingly returns home for the night. He carries a bouquet and performs some mundane tasks before looking in on a small boy sleeping in his bedroom. He pulls the covers over the boy, then the man crouches down to look over a second boy asleep in a sleeping bag on the floor, surrounded by scattered comic books. Suddenly the man claps his hand over the boy's mouth, holding him down as he wakes in terror. "Scream and I'll kill your brother," he warns him.
In 1960, Alcatraz inmate Kit Nelson - the man we've seen in the present day - is surrounded in the prison recreation yard by several fellow inmates, who severely beat him. Assistant warden Tiller watches the assault with a guard but takes no action, noting that it's only the latest beating Nelson has received. Eventually Tiller has the guards pull Nelson inside before he's killed.
Back in the present day, Doc works on his newest graphic novel: an adaptation of his latest real-life adventure. His comic book store employee Chet marvels at how great Doc's life seems - at least to a 16-year-old, notes Doc. He then hears a report on his police scanner about the abduction and recognizes it as the apparent work of Nelson. He rushes out of the store to alert Rebecca and Hauser.
Hauser watches over Lucy, still in a coma after being shot. Rebecca assumes that there's still a chance Lucy that will revive, but Hauser's silence suggests he thinks otherwise. They're interrupted by Doc, who tells them that a young boy is missing in Walnut Creek, and a chrysanthemum has been found in his bed. This detail has Doc feeling certain that the abduction is the handiwork of Nelson, one of Alcatraz's vanished '63s responsible for three similar abductions in the late 1950s. Doc is desperate to join the search. Based on Nelson's past history, the boy will be returned to his home, dead, within 48 hours.
Nelson's files reveal that his parents are dead, and his younger brother died of scarlet fever at age 11. Rebecca notes that this is the same age as the abducted boy.
She and Doc interview the kidnapped boy Dylan's mother, who recognizes Nelson's photo as a man she knows from the local hardware store who'd approached her for handyman work. Her son Liam tells Rebecca that Nelson had previously given him candy, and he'd seen him in the bedroom the night before but pretended to be asleep because he was scared. Meanwhile, Nelson takes the kidnapped boy to a lake where they rent a boat and buy fishing bait.
In 1960, the severely beaten Nelson is in the prison's hospital ward, attended by the prison doctor, who casually remarks that if Nelson wants something stronger than coffee to ease his pain he's out of luck; the doctor is a father of two young children himself. Nelson chats with the patient in the bed next to him. The patient happens to be Rebecca's grandfather Tommy Madsen, who notes that Nelson might have better luck if he befriends some fellow inmates, but he obviously does not enjoy adult company. Madsen tells Nelson that child killers are at the bottom of the prison hierarchy; he suggests that the inmates didn't beat him because of what he did but for what he is.
The hardware store manager doesn't recognize Nelson as an employee but reveals that a uniform and some children's fishing poles were recently stolen during a break-in. He points them to the nearest fishing destination, the Lafayette Recreation Area.
On the lake, Nelson fishes with Dylan a while before suddenly telling him that he has to get into the water. He tears off the boy's lifejacket and throws him into the lake. He jumps in himself, and demands that Dylan hold Nelson's head underwater for as long as he is able, and the boy complies. Nelson eventually breaks away and resurfaces, and tells Dylan, "Your turn."
Arriving at the recreation center to find an empty boat on the shore, Rebecca and Doc try to puzzle out Nelson's plan. Doc recalls a little-known report from his research detailing that in 1958 Nelson was spotted playing miniature golf with one of his victims the day before he killed the boy. Rebecca surmises that Nelson may take his victims out for something they enjoy doing before killing them - a sort of "last hurrah" - and they try to determine what other activities Dylan might enjoy. Meanwhile, Nelson has taken the boy to see a '50s monster movie.
In 1960, Warden Edwin James makes a visit to Nelson in the hospital ward, ordering him to sit in a wheelchair as he wheels him through the prison. James tells Nelson that because he's not able to determine who victimized the child killer, he's going to isolate him in solitary after he's back on his feet.
James also wants Nelson to know that the prison has received a letter from Nelson's respected war hero father asking for a visit, though Nelson has not placed his father's name on his list of approved correspondents. The warden makes it clear that he intends to allow Nelson's father to visit him. Helping Nelson out of the chair though he can barely stand, James walks off with the wheelchair. When Nelson asks how he's supposed to get back, James responds simply, "Walk."<
After determining from Dylan's mother that the boy's hobbies are not especially outdoorsy, something is triggered in Doc's mind that causes him to exclaim, "Cherry pie!" Heading to the front of the house to avoid upsetting Dylan's mother, Doc sees the police leaving after Hauser had the amber alert cancelled. Hauser doesn't want the home to look like a crime scene when Nelson returns, but Doc is appalled: it looks like Hauser is planning to let the boy die if it means capturing Nelson. Furious, Doc lashes out at Hauser's cold nature and storms off.
Hauser believes that Doc's not cut out for the job, but Rebecca defends how well he's dealing with what he's seen. When Hauser tells her that she can walk any time but she'll never find her grandfather, she angrily tells him that it's not about her personal connection to the '63s: these men are evil, and they are coming back. To combat them, Hauser needs to trust both her and Doc.
Doc enters a small diner, asking if they serve cherry pie and if Nelson had been seen there, but he has no luck. Meanwhile Rebecca tries to get Doc to answer his phone: she thinks that Doc's realized Nelson isn't doing things the victims like to do, but what Nelson likes to do. Looking at Nelson's box of belongings, she tells Hauser that Doc would see an inmate's life story in the seemingly random items.
In another diner, Doc recognizes Nelson dining with Dylan just as he receives another call from Rebecca. He answers and tries to discreetly tip her off that Nelson is there, and she races to the scene as the killer is served his cherry pie.
Back in 1960, Nelson receives a visit in the prison from his disgusted father, who tells him that his mother has died and left him something: a dried chrysanthemum. Nelson's father reveals that he suspects how during the funeral of Nelson's grandfather his mother left Nelson and his brother Elliott alone for a period and when she returned Elliott was dead from scarlet fever. But he believes that there's a different truth: Nelson killed his brother, and because his mother couldn't bear to lose both sons, she had Elliott buried immediately and lied to protect Nelson. He asks Nelson if he killed his own brother, but Nelson insists that it was scarlet fever. His father doesn't believe him and is relieved that his son will die in Alcatraz.
In the present, Nelson finished his pie and is about to leave the diner with Dylan when Doc tries to stall him by asking for change for a dollar, but Nelson refuses him. When nothing else works, Doc follows Nelson out of the diner and calls him by name, demanding that he release Dylan. Doc tells Dylan not to give up.
Rebecca arrives and draws her gun on Nelson, but he's already got his own weapon pointed at Dylan's temple. Nelson forces Rebecca to toss her gun, phone, and keys aside and handcuff herself and Doc to a dumpster. He then drives away. Rebecca pulls out a second, hidden gun and shoots through the cuffs' chain, but Doc is feeling panicked, believing that he's just caused Dylan's impending death.
At Alcatraz, Doc sorts through Nelson's meager belongings in his former cell, desperate for a clue to save Dylan within the next 12 hours. He discovers a stash of Marlboro cigarettes - a brand far more expensive and valuable than the standard prison-issue cigarettes, which causes them to wonder how someone like Nelson could afford them. Doc then finds a series of back-pay checks applied to Nelson's prison account from a new-defunct company that once built bomb shelters.
They realize that Nelson likely knows the modern-day locations of various hidden bomb shelters, and Doc identifies one in Walnut Creek, hidden where a now-demolished house once sat in a heavily wooded area. Meanwhile, in the bomb shelter, Nelson loses his temper playing checkers with Dylan.
In 1960, Tiller has Nelson thrown into "the hole," a solitary cell with no light or sound. In the dark cell, Warden James lights a match and tells him that they're going to have a conversation that's four matches long. James then describes a style of collecting items like matchbooks, and suggests that he is something of a collector himself. James then makes it clear that he'd like to deliver the truth about the fate of Nelson's brother to Nelson's father, and as the father of two children himself James plans to leave Nelson in the darkened cell until he confesses to what he has done.
On the last match, Nelson admits strangling his brother in a bomb shelter; he knew that he enjoyed it so much he would have to kill again. The flower was placed on his mother's bed as a kind of consolation prize - it was her favorite, as was her brother.
James then informs Nelson that he's not honoring their bargain, but he will allow Nelson to keep his clothes as he's sealed into the dark cell, leaving him a box of matches that he suggests Nelson make last.
Back in the present, Nelson is lost in thought remembering the lockdown with the matchbox James left him when Dylan sees an opportunity to distract him and tries to escape. A storm rages over the forest as Nelson chases Dylan into the night.
Rebecca and Doc find the bomb shelter and hear Dylan's cries for help in the distance. Just as Nelson recaptures Dylan, Rebecca gets the drop on him. Nelson tells her that she didn't shoot him before and won't now; she reminds him that he had a weapon earlier. Nelson decides to take his chances, but before he can make a move Nelson is shot by Hauser.
Later at Alcatraz, Hauser has something to discuss with Doc, and Doc allows Rebecca to hear it. Hauser suggests that Doc may be a victim of arrested development as the result of a trauma suffered during childhood. He alludes to something that happened to Doc at age 11. Hauser tells him he's on the task force because he's needed because of his unique expertise, but he's needed as an adult, not as the 11-year-old. Doc starts to tell Rebecca about his childhood trauma but freezes up. Rebecca lets him off the hook, telling him that he probably has a good "origin story."
Delivering comic books to Dylan in the aftermath, Doc reveals that when he was a kid he was also abducted, and while it wasn't easy he was able to get away too. The knowledge that you can be free "sort of gives you a superpower," Doc tells him, "like [the superheroes], but real." "I didn't give up, like you said," replies Dylan.
Hauser carries a body bag into the secret prison facility, delivering Nelson's remains to Dr. Beauregard. Hauser tells Beauregard that he may need him to help him with a favor for a friend, and Beauregard readily agrees. As Hauser leaves, the doctor puts a cigarette in his mouth, begins to play a record on an old turntable, and sets merrily about his grisly task.