In modern day San Francisco, a handsome man in a business suit enters a bank carrying an attache case; he asks to see his safe deposit box. He's led back to a secure area of the bank by a teller, Amanda, and once out of sight they passionately kiss. But just as things begin to get steamier after the security cameras are deactivated, the man sedates the teller with a hypodermic needle.
Using a special tool, he blows out the locks of several safe deposit boxes and begins looting them, finding a particularly valuable-looking sapphire necklace in the process. When he's interrupted by an unsuspecting bank employee, he pulls a weapon, holding it to the employee's head.
The scene shifts to the Alcatraz laundry room in 1960, where the bank robber - Cal Sweeney - instructs a new inmate on how contraband is smuggled to the prisoners in the pockets of clothes sent for cleaning. The younger inmate offers a package of clothes to a third inmate, who says that he's cash-short and hopes to pay the following week. Sweeney agrees, but triples the price, telling the younger inmate that since he takes the risks, he calls the shots: he refuses to be seen as weak or to show any emotion. Revealing a soft spot, he believes, leads to failure.
Returning to his cell after learning that the guards have searched it, Sweeney desperately seeks out a crucial hidden item. When he fails to find it, he asks to speak to assistant warden Tiller.
Back in the present day, Rebecca and Doc share dim sum for breakfast, as Doc explains how a man with two PhDs ended up owning a comic book store. He got his degrees to please his parents but was blacklisted for publishing an article about a controversial crime prevention theory - controversial because he based his statistical model on Batman's Gotham City. Rebecca realizes that Doc intentionally humiliated himself academically rather than simply quit and face his parents, to which he adds simply, "It's a complicated relationship."
Receiving a call about the bank robbery, Doc immediately thinks of Cal Sweeney, and he tells Rebecca that robbing safe deposit boxes is a lesser crime than robbing cash from banks because the boxes aren't FDIC-insured and thus their theft is not a federal offense. Hauser tells them that that six boxes were hit, and the dead employee in the vault was murdered with a weapon used to kill cattle in slaughterhouses.
Rebecca interrogates the bank teller Amanda, who reveals that she first encountered Sweeney in a grocery store and was quickly seduced; she never met him at his own home or saw his vehicle. Doc discovers that Sweeney hit a bank a few days earlier and must have spent the intervening time pawning the items he stole, but banks don't keep track of safe deposit box contents.
Meanwhile, Sweeney poses as a bank employee and visits the owners of the boxes he's pilfered, pretending to get an inventory of the items inside to help evaluate the contents. He learns the value of the sapphire necklace from its owner, William Bailey, who tells him that it was a gift to his wife for their 25th wedding anniversary.
The owner grows suspicious when Sweeney asks where the man met his wife. Sweeney tells him, "I need to know for me," showing him the necklace. He then shoots the man through the hand with his bolt pistol. He demands to know the full story.
Back in 1960, Tiller receives a shave while he meets with Sweeney, who wants to know the location of the item missing from his cell: a small metal box. Tiller pleads ignorance and instead wants in on Sweeney's contraband operation. Sweeney refuses to cooperate until his stolen item is returned, leaving Tiller to manage the disgruntled prison population when they don't receive their forbidden perks. Accidentally cut by his barber, Tiller explains that the secret to a good shave is to go with the grain - when you don't, that's when you get nicked. His message clear, and he has Sweeney returned to his cell.
In the laundry room, Sweeney tells his protégé, Harlan, that he can't allow Tiller to get away with this or it will be perceived as a sign of weakness. Harlan suggests a deal that wouldn't cause a loss of face: he suggests that Sweeney try to arrange steward's duty at a party for Tiller's birthday thrown by Warden James at the warden's house.
In the present, Rebecca and Doc realize that most of the safe deposit boxes' contents are legal documents and otherwise unremarkable items valuable only to their owners. Arriving at the Bailey home, they encounter Bailey's wife, Melissa, who lets them inside, where they discover him murdered on the floor. Meanwhile, Sweeney arrives at another bank and waits in line, giving a knowing wink to yet another besotted female teller.
In 1960, tuxedoed Sweeney and Harlan precisely arrange the dining table at the warden's residence while also assuring each other that they're clear on the details of their plan. Meanwhile, Warden James tells them that he hopes to give Tiller a night he'll never forget.
Tiller arrives with his sister, Geri, who has both cerebral palsy and a sharp sense of humor. Also at the dinner is Lucy, in her 1960 persona as Lucille Sengupta, a medical doctor and psychologist. She reveals that her work at Alcatraz includes attempting to remove traumatic memories that led inmates to their lives of crime. She wants to replace these memories with more soothing ones, with the goal of eliminating the inmates' antisocial tendencies, though Dr. Beauregard is derisive about her theories. Harlan quietly tells Sweeney, "Now they want to steal our memories, too."
In the present, Rebecca and Doc go over Sweeney's Alcatraz belongings, finding nothing but an empty metal box that looks it was burned in a fire. They tell Hauser that Sweeney appears to be visiting one of the box owners from each of his robberies, leaving them dead - something he never did in the past.
Desperate for a means to track him, Rebecca zeroes in on Sweeney's seduction of the bank tellers. Security videos reveal that in both robberies the tellers he conned had the same type of flowers on their counters, and after a quick investigation they discover a third floral delivery had been sent out to another bank.
Meanwhile, Sweeney has the latest teller in the safe deposit vault. She sees the needle in his hand before he can drug her, and she sounds an alarm. Sweeney is still able to loot several boxes and tries to coolly walk out of the bank, but it's on lockdown after the alarm went off.
Sweeney knocks out a guard and steals his gun in an attempt to leave, but his path out the door is blocked by the arrival of police cars. Sweeney fires the gun into the air and orders everyone inside the bank to get down, just as Rebecca and Doc arrive.
In 1960, Warden James raises a glass in toast to Tiller, who opens his gift: a high-end pen. Harlan spills hot coffee on Tiller, enraging him, but the guests urge him to calm down. As Tiller cleans up in the restroom, Sweeney confronts him and offers a tiny percentage of his business in return for his box, but Tiller demands 50 percent. Seething, Sweeney agrees and demands the box, but Tiller still insists that he doesn't have it.
Sweeney furiously begins to beat Tiller and dunk his head into the toilet, insisting that he reveal the location of the box. Tiller ends the struggle by stabbing Sweeney in the leg with his new pen. Composing himself, Tiller instructs Sweeney to stay where he is until someone arrives to collect him and deposit him in "the hole" for 30 days - assuming he doesn't bleed out through the night.
Back in the present, Hauser tells Rebecca that he'll run interference by haggling over jurisdiction to buy her time to get inside the bank. Doc suggests that due to the unique construction of old buildings in San Francisco, she may be able to get inside the bank through the air conditioning vent from an adjoining building, but she'll also trigger an alarm that will keep her from exiting as stealthily. Believing that if she goes in armed Sweeney will kill her, she leaves her weapons behind.
Waking up his teller paramour, Sweeney demands that she help him get out of the bank or he'll kill everyone inside, but she has no answers for him. Rebecca's arrival draws his attention, and he holds her at gunpoint as she tells him that she's there to break him out.
Rebecca's knowledge of Sweeney's identity persuades him to go along with her. Outside, Hauser argues jurisdiction with the local police until they hear gunfire from inside the bank, and the police take action, launching gas grenades into the bank and sending in a team to retrieve the hostages. Rebecca emerges from the bank accompanied by a police officer in riot gear - Sweeney in disguise - and they drive off in a police car.
Doc drives up to Hauser in Rebecca's muscle car, and they speed off in pursuit, with Hauser criticizing Doc's driving: he hasn't been behind the wheel since he was 11 years old.
Sweeney tells Rebecca that she's his hostage now. He notices Doc and Hauser following, and Hauser orders Doc to trust Rebecca and break off pursuit.
In 1960, Sweeney and Harlan are in adjoining cells as Sweeney frets about how he's going to endure 30 days in the hole. Harlan tells Sweeney that he's sure it was worth it: "If I had lost my whole family and everything I ever had when I was only ten in a fire, I'd sure want to hold on to the one single thing that didn't burn . . . even if it was just an empty tin box." Harlan slides the box over to Sweeney's cell.
As Harlan taunts Sweeney with the knowledge that he doesn't have a single thing to his name to remind him of his childhood and family, Sweeney realizes that Harlan was the one who'd set him up all along. Harlan says that Sweeney broke his own first rule by revealing his own vulnerability. When he gets out of the hole, Harlan will be running the contraband operation himself, and no one will even remember Sweeney was there. Sweeney places the box on the floor of his cell and crushes it with his heel, leaving it behind as he's taken away to solitary.
In the present, Rebecca wants to know what Sweeney took that was worth all the trouble. He holds up a black leather pouch - he has no idea what's inside. She suggests that he open it, but he says he not supposed to, although he doesn't know why.
Agitated, he tells her to pull over so he can release her. She notices that he hasn't buckled his seat belt, so she accelerates and crashes into a parked car, knocking him out long enough to disarm and handcuff him.
Back at Alcatraz, Doc adds Sweeney's mug shot to the wall of captured inmates. Rebecca realizes that they still have a long way to go. She shows Doc the black pouch, which contains a key, which Hauser arrives to claim. But Rebecca wants to know what it's for before handing it over. Hauser takes it and says he'll tell her another day.
Hauser takes the key to a science team in a hidden section of Alcatraz, telling them that they have another one to add to the key they'd previously collected from Jack Sylvane. He suggests a molecular analysis to determine how the prisoners time-jumped, which reveals that the keys were laser-cut and could not have come from the 1960s. Hauser launches a full investigation as to what the keys open.
Back in 1960, Warden James escorts Harlan into a dark, secluded area of the prison, and while Harlan initially thinks it has something to do with Sweeney ratting on him, the warden suggests that someone else wants to speak with Harlan. James uses two of the familiar keys to unlock an elaborate lock system - along with a third - and pulls open a heavy metal door.
"Your future just got a heck of a lot brighter, kid," James tells Harlan, and he pulls him inside. "Don't be shy."