Against a vision of the Alcatraz Island prison facility in the foggy San Francisco Bay, Emerson Hauser recounts in voiceover the closing of the prison on March 21, 1963, and the relocation of its many notorious prisoners. "Only that's not what happened," adds Hauser. "Not at all."
The scene shifts to a night in 1963 when two uniformed guards disembark the ferry to Alcatraz, only to find the entire prison deserted. They explore the facility with flashlights and guns drawn, but every cell, office, and guard station appears to be abandoned. Hauser recounts that 302 men disappeared that night, never to be seen or heard from again.
In the present day, tour groups visit the long-defunct prison, and a young girl slips away to explore on her own, making a startling discovery in one of the cells. Alerted by her screams, the tour guide finds a man lying on the floor of the cells - the guard tells the man that he can't sleep there. The man steps from the cell into the sunlight, looking shaken and confused as he sees the dramatic San Francisco skyline from the island. He boards the shuttle back to the city and thumbs through a souvenir booklet filled with photos of the long-ago inmates; soon he finds his own mug shots within.
The scene shifts to 1960, when the man is revealed to be an inmate named Jack Sylvane. He's called over by the associate warden E.B. Tiller, who orders guards to search Sylvane's cell. They declare it clean, but Tiller enters and claims to find a screwdriver hidden away behind a framed photo of a beautiful woman. Sylvane denies that the tool is his, but Tiller has him placed in solitary - even though Sylvane was expecting a visitor. Back in the present day, paging through the booklet, Sylvane sees a photo of an aged Alcatraz official at his retirement home - a man identified as Tiller.
In the Bay, two wet-suited swimmers race between buoys. When they emerge, the loser of the race, Rebecca Madsen, bristles at having been beaten and being told by her fiance, Jimmy, that she doesn't save her energy for the all-important final surge. Later, arriving at her job as a San Francisco police detective, it's clear that she patiently endures much ongoing locker room hazing from her colleagues as one of the few women on the squad. She pays Jimmy her debt on the race, thanking him for never letting her win.
Called to a homicide scene, Rebecca investigates the murder of an elderly man named E.B. Tiller, noticing a smashed photo of Tiller and another man on his mantle. Suddenly, an enigmatic government agent named Emerson Hauser enters and announces that because Tiller was a longtime federal employee, his agency will be taking over the investigation from the local police.
Rebecca refuses to leave a crime scene unless ordered to by her immediate superior, then almost immediately she receives a call from her lieutenant with the bad news. She quietly asks Jimmy to run Hauser's name through their databases while she does some investigating of her own: finding a fingerprint on the broken photo, she IDs it as belonging to Jack Sylvane, but she discovers that computer access to his criminal file is restricted.
In the lab, Rebecca is approached by Lucy Banerjee, a government agent on loan to the department. Lucy's simple Google search identifies Jack Sylvane as an Alcatraz inmate and Tiller as a former warden. Much of the online research they find is written by Alcatraz expert Dr. Diego Soto, and Rebecca decides to seek Soto out.
Rebecca finds Diego in a comic book store playing video games and questions him about Sylvane and Tiller. Diego tells her that Sylvane was "one unlucky cat," a World War II veteran who was sent to Alcatraz for robbing a grocery store in desperation, only to be sentenced to federal prison because the store sold stamps and was technically considered a government post office. Sent to Leavenworth and forced to kill an aggressive fellow prisoner in self-defense, Sylvane was transferred to the Rock. Diego says that it's impossible for Sylvane's actual print to be at the scene of Tiller's murder because the inmate died more than 30 year earlier.
Another flashback to 1960: Tiller releases Sylvane from solitary, and Sylvane demands to know what Tiller told his wife. Tiller torments him by saying he's made a mistake and it's not time for him to be freed yet. "Remember, this is Alcatraz," Tiller reminds him. "Things can always get worse."
Back in the present day, Sylvane purchases a day at a gym and enters the locker room already possessing a key: he unlocks one of the lockers and retrieves a gun. Discovered by an unsuspecting attendant, Sylvane grabs him and throws him roughly into the lockers, knocking him out.
Rebecca visits her surrogate uncle, Ray Archer, a former Alcatraz guard who now tends his own bar; she asks what he knows about Tiller. Ray tells her that Tiller was a hard case who rose through the administrative ranks but got out before the prison shut down.
Diego arrives and immediately recognizes Ray as an Alcatraz guard from his research and is honored to meet him. Rebecca explains that Ray essentially raised her after the death of her parents, and she reveals that her grandfather was also an Alcatraz guard named Tommy Madsen, a name that prompts a nervous recognition from Diego. Diego produces paperwork documenting Jack Sylvane's transfer to San Quentin - signed by Robert Kennedy - as well as death certificate, but Rebecca wonders if they've been faked.
Ray tells her that Tiller worked for a federal agency after leaving Alcatraz and reminds her that this is now not her case to be investigating. She resists, but Ray urges her, for once in her life, to just walk away. As Ray leaves, Diego tries to diffuse the awkwardness by revealing that his very smart Stanford faculty parents are always telling him what to do, but mostly he simply listens to their advice and then does what he wants to anyway. He says that the last time he was on the island he found a room filled with files that he wasn't supposed to see, and he agrees to join her in continuing her investigation with a visit to Alcatraz.
Jimmy tells Sarah that he couldn't find any records about Hauser's federal service, but despite the mystery he worries that she's pursuing the case primarily in an attempt to learn more about her family and its ties to Alcatraz. Her grandfather Tommy died 20 years before she was born, and all she knows about him he learned from Ray: he loved J.D. Salinger and Tootsie Rolls, and that's about it.
Diego arrives to join Sarah, and he and Jimmy give each other the once-over. On the ferry to Alcatraz, Sarah explains that she spoke with the San Quentin warden to confirm Sylvane's transfer, but there's still something odd about the case: Sylvane was a thief, not a murderer. Diego also wonders, if Sylvane was indeed still alive, why he would wait so long to kill Tiller.
Rebecca and Diego slip off from visiting the barracks where the guards lived with their families on the island. Still possessing a key he shouldn't have, Diego unlocks the door to the secret storage room he previously discovered, where the inmate files still remain. Diego shows her that personal items from the inmates are also stored there.
Then an unexpected noise reveals that someone's watching them. As Rebecca draws her weapon to investigate, a canister spewing gas drops into the storage room, knocking them both unconscious. Later, a groggy Rebecca revives and finds herself face to face with Emerson Hauser, who welcomes her to Alcatraz.
As Diego also revives, Hauser explains that, while he's admired Diego's books on the prison, he had to follow strict protocol on how to handle intruders. Rebecca is surprised when they're joined by Lucy, who actually works for Hauser. Hauser explains that he heads a special division of the government that has a particular interest in certain fugitive prisoners. In Hauser's secret facility, Rebecca notices a computer-generated image of what Jack Sylvane should look like at age 85, but Lucy shows her surveillance video from the night of Tiller's murder revealing that Sylvane still looks as young as he did while serving time on the island. Before Hauser or Lucy explain the seemingly impossible situation, they receive an alert about an Alcatraz-issue uniform that's been discovered at a crime scene. Hauser decides to let Rebecca and Diego join them in their investigation.
Flashing back to the past, Sylvane has been released from solitary after a month, handcuffed to a bed in the prison's medical ward while an ill-tempered doctor draws his blood - even though Sylvane knows he not sick. Sylvane grows irritated when another patient in the bed next to him, hidden in shadows behind a partition, cheerfully whistles, and he threatens violence if the man doesn't stop. The other patient - Inmate #2002 - remains nonchalant and unsympathetic to Sylvane's having missed his wife's visit when he was wrongly put in solitary, telling Sylvane that he's probably better off because "something terrible's going to happen here."
The assaulted locker room attendant gives Hauser, Rebecca, and Diego a description of his assailant as well as the license plate number of the cab Sylvane escaped in. They track it to an address, where uniformed officers are dispatched to intercept Sylvane just as he arrives. Sylvane opens fire on the police, while inside the home a gray-haired but also youthful-looking man named Barclay Flynn grows fearful. Making it past the police, Sylvane pursues Flynn inside the home, pulling a gun and demanding that Flynn open a hidden safe. Flynn complies and gives Sylvane a black bag within, only to be executed by Sylvane.
Hauser, Rebecca, and Diego arrive on the scene to discover the injured officers and the dead Flynn. Hauser tells Rebecca that he believes Sylvane's acting on some kind of direction, while Diego reveals that Jack's wife remarried after his seeming death - specifically, to Jack's brother.
The wife is dead, but the brother isn't, and Rebecca suspects that he may be next on Sylvane's hit list. She decides to break away from Hauser to intervene, believing that Hauser will never shed any real light onto the situation. Meanwhile, Jack knocks on the door of Alan Sylvane, Jr., his brother's son. Photos of Jack's wife later in life fill the apartment, and he remembers their last visit on Alcatraz where she tearfully asked him for a divorce. He flew into a rage and was removed by the guards.
Back in the present day, Jack learns that she died two years earlier, and he tells Alan, Jr., he has his mother's eyes. When Alan, Sr., sees Jack he is stunned with recognition. Alan, Sr., doesn't understand why Jack is there and how he's still so young. Jack still agonizes over his wife and brother's betrayal, clutching his gun purposefully.
Minutes later, Rebecca and Diego arrive and discover Alan, Jr., bound and gagged - Jack has left with Alan, Sr., forcing him to take him to the cemetery where his wife is buried. At her graveside, Jack forgives her, but the "reunion" is short-lived: Rebecca holds Jack at gunpoint. Sylvane admits killing Tiller out of hatred, but he says that he only killed Flynn because he was doing what "they" told him to do.
Rebecca wants to know who he's talking about, but he simply asks her to shoot him, pulling a gun to force her hand. She tries to talk him down, but suddenly Sylvane is shot; Hauser has arrived and one of his snipers wounded Sylvane, whom Hauser takes into custody. Sylvane tells Rebecca that she should have killed him.
At his agency headquarters, Hauser tells Rebecca and Diego that Sylvane is back in prison under a new identity for a life sentence, and that his brother "won't be a problem." Rebecca says that her investigation on Barclay Flynn revealed no ties to Sylvane or Alcatraz, but Hauser says that he's certain Flynn will be tied to "our next victim," which confuses Rebecca.
When Lucy adds that a new Alcatraz uniform has turned up, Rebecca realizes that somehow Hauser knew all of this was going to happen and was waiting to intervene for a long time. "A very, very long time," adds Hauser, who reveals a room documenting the "the '63s": photos and files on 256 prisoner fill a wall on the right, while 46 guards are depicted on the left wall. The closing of the prison and the prisoner transfers are an elaborate cover story, he tells them.
Back in 1963, the two guards who discover the empty prison prepare to alert the authorities back on shore. The senior guard asks the name of rattled younger guard: "Emerson Hauser," the young guard replies. In the present, Hauser tells Rebecca and Diego that Alcatraz's criminals are coming back, and coming back to a world in which they do not exist - Jack Sylvane was just the beginning. As she scans the wall, Rebecca makes a startling discovery: her grandfather Thomas Madsen was not a guard as she had believed - he was a prisoner.
She realizes that Hauser wanted her involved all along, piquing her interest and testing her resolve by kicking her off the case. Hauser offers to add her to his task force, but he warns her that it will be hard on her: to keep them out of danger she can't tell Jimmy or Ray what she's doing. Rebecca agrees, asking that Diego also be included. After accepting Hauser's offer, Rebecca wonders why Uncle Ray has deceived her for so long.
Meanwhile, Hauser and Sylvane travel to a secret outpost hidden among the redwoods, a prison where Sylvane will be incarcerated. Even though Sylvane agrees not to give Hauser any trouble, Hauser strikes him. "E.B. Tiller was my friend," says Hauser, who leaves Sylvane to be locked in his cell by the guards. "Not to worry, Jack," adds Hauser. "You won't be lonesome long."