Lucy, freshly revived from her comatose state, reviews multiple video interviews with the recaptured Alcatraz inmates. She zeros in on Ernest Cobb, the prisoner who shot her, until she's interrupted by Hauser.
Hauser chides Lucy for not taking it easy during her recovery. She says she wants to catch up with what's happened since she was incapacitated, but he tries to prevent her from joining him in meeting with Rebecca and Doc. When Dr. Beauregard balks at giving her a clean bill of health until any side effects of her blood transfusion from inmate Webb Porter can be determined, she chooses to go anyway, on her own.
The driver of a parked armored security vehicle is surprised after clearing the security badge of another guard outside the truck, when he is quickly ambushed and overcome by a rifle-toting, uniformed man. The impostor then gets the drop on a pair of returning security guards, who are surrounded by his masked accomplices. The ambush team dons the guards' uniforms and disable the truck's GPS tracking system, ejecting the guards and driving off.
In 1960, inmate Garrett Stillman - the leader of the present-day armored truck ambush team - plays chess against himself in the Alcatraz recreation yard. Warden James approaches him and completes a move, wondering which of the chess pieces Stillman favors. The warden is surprised when the highly intelligent Stillman names the seemingly limited bishop, but the inmate explains that he prefers the long diagonal play after lying in wait. The warden invites Stillman to attend a parole board hearing, offering a pawn as a mysterious example of what Stillman stands to gain.
In the present day, Lucy is welcomed back with a hug from Soto, though he remains apprehensive about the secrets she and Hauser have kept about her past. After Rebecca offers her a dossier on the recaptured '63s, Lucy apologizes for her lack of full disclosure. Doc admits that despite all his Alcatraz research he's never discovered any reference to a female prison psychologist. Lucy suspects that Warden James chose to make her presence there a secret. She admits that she worked to help the inmates, including Rebecca's grandfather Tommy Madsen.
Lucy explains that after the time-jump, it's surprisingly simple to adapt to the new environment and technologies, but it's much harder to adjust to the fact that your loved ones have lived without you for so long. "While you're in their world, you're not OF their world," she says.
Lucy is impressed with the upgrades that Doc has made to the task force's search engines. She then spots an armor car heist report with some telltale features that quickly lead her and Doc to the culprit: Stillman, a British ex-military strategist with a long history of successful, elaborate, and meticulously plotted armored car heists.
Meanwhile, Stillman drops off his crew and says he plans to meet them at a rendezvous point. After the crew members climb into a van with the stolen cash, the van explodes, apparently killing them all. After eliminating his accomplices, Stillman coolly drives the armored truck away on his own.
When they examine the scene of the explosion, Doc suggests that Rebecca is being extra nice to Lucy in hopes of getting closer to apprehending her grandfather Tommy. At the scene, they discover that one of Stillman's crew has barely survived the blast and is critically wounded. Trying to puzzle together why Stillman would leave the guards alive but torch both his own crew and the money they stole, Rebecca and Doc wonder if he was actually after the armored truck itself.
Rebecca and Doc question the guards at the security company, and they discover that the business has recently had two additional armored trucks stolen. They also learn that Stillman was using a valid security badge containing security codes that are impossible to counterfeit.
Finding Lucy studying Cobb's file, Hauser tells her that she's welcome to speak with him any time - perhaps she can get more out of Cobb than Hauser did. Lucy tells him that Madsen appears to have been a crucial addition to the task force, but Hauser believes that Rebecca's tendency to make everything personal is a flaw that could be exploited by their enemies. Lucy points out that Hauser doesn't see that he used to be just like her once.
Warren, a member of Hauser's scientific team, reports that their scans have found a hollow area underneath the Alcatraz lighthouse. Lucy explains that it's a locked, secret bulkhead that was there in 1963. Hauser orders the team to locate it.
The surviving member of Stillman's crew identifies him for Rebecca and Doc from his hospital bed. He says that Stillman set up a phony sweepstakes that sent one of the security company guards on vacation and allowed Stillman to comb the guard's apartment for the active badge. The wounded man also reveals that Stillman appears to be working with a mysterious accomplice, a "handler." Rebecca suggests that it might be the same person who has provided key items to several of the other '63s.
As Stillman delivers the armored truck, he flashes back to a parole hearing in 1960. An inmate named Harlan Simmons pleads his case of good behavior, but Assistant Warden Tiller points out Simmons' prison history of brokering contraband, and the board denies him parole. After the hearing, Warden James asks how Stillman enjoyed what he saw, and Stillman notes that Simmons never had a chance of parole as long as Tiller collects a large percentage of his prison business. Warden James reveals that he prefers to have Simmons off Alcatraz sooner rather than later, and he attempts to persuade Stillman to steal the board's recommendation and replace it with a more favorable one.
"You're a man who doesn't trust people, and that means you can be trusted," says James, who offers Stillman the contraband operation with a much smaller percentage taken by the officials. He says that the parole board will be staying for lunch as James' guests, giving Stillman three hours to make his play.
In the present day, Stillman meets with his unseen accomplice, who casually slices an apple as they talk: a new crew has been arranged for Stillman's next job - though he questions the wisdom of having torched the $100,000 score from the last one. Leaning out from the shadows, Tommy Madsen tells Stillman, "You worry about the chess pieces. I'll worry about the board."
Rebecca asks Lucy about Tommy, and Lucy reveals that, like most of the inmates, Tommy could be charming but also ruthless and manipulative in pursuit of what he wanted. She also comments on his extreme patience, as evidenced by his ability to completely peel the skin off an entire apple in one piece. Hauser thinks that Tommy is important, Lucy adds, but he doesn't know why.
When Lucy reveals that she knew Hauser when he was a rookie cop, Rebecca realizes that Lucy and Hauser were a couple. For the past 50 years, Hauser was trying to find Lucy, not the inmates, and now she's trying to find what remains of the Hauser she once loved.
Meanwhile, Doc discovers that Broadway Mutual, the bank targeted by Stillman, was founded by former inmate Harlan Simmons. Simmons is now widely known as a reclusive billionaire and financial wizard who hasn't been seen in public since the 1970s.
In 1960, Stillman assembles a handpicked crew of three inmates within the prison to pull off the warden's task. He lays out his plan: an inmate on custodial duty retrieves from the wastebasket carbon copies of the parole board's forms, which provide a reference for a forgery expert to create new paperwork with authentic-looking signatures. The forger then hides the papers in a laundered uniform, which he delivers to Stillman. The third inmate will be working lunchtime steward's duty at the warden's home, where he'll admit Stillman to secretly switch out the papers.
In the present day, Rebecca and Doc learn that Simmons' bank doesn't use its vaults and armored vehicles to move much cash, which makes them wonder what's so valuable that they contract such a high security firm to transport. The bank manager doesn't know and does little to encourage Rebecca's thought of questioning Simmons himself because Simmons' legal team will likely stall even a warrant indefinitely.
As Rebecca and Doc leave, the bank manager texts instructions to Stillman and his new crew in a van, providing them the location of their next job. When one of the men asks what the score will be, Stillman coolly shoots him and dumps his body outside the van.
After Warren finds the wall that appears to hide the secret chamber, Hauser orders him to assemble the scientific team and use a sledgehammer if necessary to find a way in. Meanwhile, Doc and Rebecca's records search shows that the bank routinely moves an unspecified package from location to location once every month. Together, the task force reasons that Stillman stole the armored truck to make the bank nervous and prompt an early, unscheduled move of the package - which they discover is happening right at that moment.
Lucy encourages Hauser to join Rebecca and Doc in the field while she conducts her first inmate interview with Ernest Cobb. Hauser believes that he should be present, but Lucy insists on doing it herself.
In 1960, Stillman arrives at the warden's home with the falsified paperwork. While the warden distracts the parole board with conversation, Tiller notices Stillman's appearance as one of the stewards. After Stillman has made the switch, Tiller confronts him, wanting to know exactly when he started on steward's duty. This prompts Stillman's accomplice to reveal the entire plot in hopes of avoiding punishment.
Meanwhile, in the present day, Stillman and his crew are ready to make their heist. When a security guard is alerted as Stillman's badge registers as invalid, Stillman draws his gun and knocks the guard unconscious. Hauser and Rebecca arrive in time to pursue the fleeing armored truck into a parking garage.
In 1960, Warden James watches as Tiller sees the parole board off at the docks, then he joins Tiller, feigning annoyance at being summoned for such a routine sendoff. Tiller explains that he discovered Stillman's scheme and had sent the board back to the mainland with the proper paperwork denying Simmons his parole. James pretends to be pleased by Tiller's fast action. He later accompanies Stillman to his new berth in D block, telling Stillman that he's disappointed in him - he failed to seize his opportunity to step to the top of the food chain at Alcatraz.
Stillman tells James to check the envelope confiscated by Tiller. When the warden sees that the paperwork is in fact the original forms denying Simmons parole, James realizes that Stillman actually did make his plot work, using Tiller to unwittingly make the switch after Stillman reasoned that he'd never have time to get past the briefcase locks.
Everything played into Stillman's plan, down to the well-known snitch on steward duty. James admits Stillman had him going and wishes him well until he's removed from D block in 30 days.
The task force searches the parking structure for a sign of Stillman when suddenly all three of the stolen armored trucks are in sight and on the move. Taking advantage of the distraction as Rebecca and Hauser give chase, Stillman calmly loads his package into a hot-wired SUV. All the while, Doc observes from a discreet distance, having puzzled out Stillman's next play and informing Hauser and Rebecca that he's hidden his cell phone - with its GPS tracking capabilities - on Stillman's escape vehicle. Believing that he's made his escape, Stillman retreats to his hideout and opens the package, revealing a key inside.
In 1960, Warden James sees off Simmons as he prepares to start his life anew. The warden cautions him to remember the lessons he's learned during his time on the island. James also provides Simmons with the number of a friend who'll help Simmons get on his feet and who will also put the warden in touch when the right time arises. As Simmons sails back to the mainland, Warden James studies the same key that Stillman possesses in the present day.
Stillman's study of the key is interrupted by unexpected arrival of a gun-toting man Stillman recognizes; the man tells him that he wasn't supposed to open the package. Stillman replies that he didn't steal it for the man, whom he calls "Ghost," and he doesn't intend to give it to him now. "I guess I'll have to take it," the man replies, firing his gun.
After Rebecca and Hauser track Doc's phone to Stillman's airstream trailer hideout, they find him there, dead from a gunshot. Next to his body is the complete peel of an entire apple: Tommy Madsen's trademark. Outside, Doc spots a vehicle slowly approaching. Doc can't make out the driver, but it's Tommy. As soon as he catches sight of Doc, he blinds him with the vehicle's bright headlamps and drives away.
Back beneath the lighthouse, the scientific team has cleared away enough of the wall to reveal the thick metal door glimpsed in the past, giving Hauser an opportunity to test the two keys he's found while pursuing the '63s. When he tries them in the locks simultaneously, a secret panel opens revealing a third keyhole.
Meanwhile, Lucy interviews Ernest Cobb, calmly asking why he shot her. "You were a target," he replies. At first Lucy thinks that the inmates are aware of the entire task force and intend to eliminate him, but Cobb explains that the only target is Lucy, and she'll remain one as long as she's alive.
Rebecca and Doc search for clues to the identity of the driver of the vehicle they saw, prompting Doc to download images from a traffic camera on the car's probable route. After a quick scan through the photos, Doc spots the car in question. Tommy Madsen's face is clearly visible behind the wheel, leading Rebecca and Doc to believe that he's the handler behind Stillman and the rest of the '63s.