The scene opens and 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 San Francisco, police detective Rebecca Madsen is in a rooftop pursuit with her partner, chasing a crew cut-sporting suspect. When her partner ends up dangling from the rooftop's rain gutter, Rebecca has to choose between catching the criminal and saving her fellow officer. She tries to make the rescue, but the rain gutter breaks away, and her partner plummets to his death. The scene shifts to the current moment, where Rebecca is roused from the memory by her superior officer, who's attempting to insist that, after three months of working solo, she choose a new partner. She rejects the likely candidates for trivial reasons, and her boss urges her to stop feeling responsible. She says that she blames the suspect they were chasing, but all leads to him have ended cold.
She does promise to pick a new partner within the day, however. 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, a uniformed officer, 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.
A simple Google search leads her to info on Sylvane and Tiller, connecting them to Alcatraz, and she decides to seek out Alcatraz expert Dr. Diego Soto. Rebecca finds "Doc" Soto in a comic book store playing video games and questions him about Sylvane and Tiller. Doc 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. Doc 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.
Doc arrives and immediately recognizes Ray as an Alcatraz guard from his research and is honored to meet him. Doc 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, Doc 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. 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. Doc also wonders, if Sylvane was indeed still alive, why he would wait so long to kill Tiller. Rebecca and Doc slip off from visiting the barracks where the guards lived with their families on the island. Still possessing a key he shouldn't have, Doc unlocks the door to the secret storage room he previously discovered, where the inmate files still remain. Doc shows her that personal items from the inmates are also stored there.