During a tour of Alcatraz, the hulking former inmate Pinky Ames walks the prison's halls with intent, lingering at his old cell as if searching for something. His memories draw him back to his incarceration in 1961, where he joins his brother Herman - apparently his much slighter but more verbose fraternal twin - in the prison mess hall. Herman is arguing over baseball with another inmate.
Pinky plays the role of Herman's enforcer, threatening physical violence unless the inmate leaves his spoon behind. Failing to turn in all his silverware is an act that will land the inmate in the Hole. "Better than the infirmary," Herman says. The brothers then plot to "make a move" in a scheme masterminded by another inmate, Donovan. They don't trust Donovan, but they believe that his risky plot will make them rich when they walk out of Alcatraz.
Back in the present day, Rebecca and Doc are at Alcatraz. They are secretly watching one of Hauser's scientists through security cameras while he conducts experiments in the middle of the night. As Doc moves in to observe firsthand, an electric storm begins to rage outside the prison, and Pinky Ames appears in the cellblock, brutally killing the scientist. Hidden in the hallway, Doc recognizes Pinky dragging the body away but is surprised when he's confronted by Herman.
When Doc doesn't return to the control room as planned, Rebecca grows concerned. Learning that Doc is an expert on Alcatraz, the Ames brothers quiz him about themselves. Doc explains that he knows that they made a legendary escape attempt in 1961, but he never understood exactly how they planned to get off the island once they were out of their escape tunnels; the details had always bothered Doc. When he mentions their "antiquated" maps, they present him with a new one made from memory. They want him to update it for them. Suddenly, Doc realizes that the brothers had an accomplice and they weren't trying to escape in '61. They were trying to locate a rumored stash of gold hidden in the prison.
In '61, Warden James is praised by Father Gordon, a Catholic priest, for his attempts to reform the prisoners by allowing them to attend Sunday services. Tiller, however, suggests that the prisoners show up solely for an extra hour out of their cells. Pinky is an altar boy, and he tells James that he's committed to saving his own soul, though he says he's more spiritual than religious. "Spirituality is for those seeking understanding; religion is for those seeking reward," Pinky says. Taking the warden's coat, Pinky discreetly slips a set of keys from its pockets, then meets with Donovan - a prison guard - who watches the kitchen door as Pinky presses the keys into bars of soap to make molds of them.
Back in the present day, Rebecca searches for Doc in the prison. A bloody streak leads her to the hidden body of the murdered scientist. Hauser arrives to find the control room empty. When he turns on the security cameras, he reviews the tape and sees everything that's happened. Then the Ames brothers lock Doc in the Hole, refusing to reveal who their accomplice was.
In '61, the brothers work in the Alcatraz kitchen, using utensils there to make their own key copies from the molds as Donovan stands watch. When the shift change starts the brothers need more time to complete the keys, so Pinky stages a distraction by causing an accident, pushing another inmate's pinky finger into the meat slicer. The brothers' scheme goes undetected, but guard Ray Archer's suspicions are raised by metallic residue they leave behind.
In the present, Rebecca gets the drop on a shadowy figure, holding him at gunpoint. Claiming to be an Alcatraz security ranger who's tracking two armed men who stayed behind after the last tour, he tells her that his name is Donovan.
At Sunday service in '61, Warden James delivers a homily to the inmates about redemption, when he's interrupted by Herman giggling uncontrollably. Believed to be drunk, Herman is strong-armed out by Donovan; Pinky's attempts to quiet Herman lead him being ejected as well. Both brothers are thrown in the Hole.
Ray shares his suspicions about the Ames brothers with the warden, explaining that while they're violent, they're also cunning. Their behavior suggests that they're up to something, Ray says. James goes to question the brothers in the Hole, and he's stunned to find instead a badly beaten Donovan imprisoned inside.
In the present, Doc uses his cell phone while imprisoned in the Hole; he's only able to contact his comic book shop employee Chet. Doc instructs Chet to look up whether the Alcatraz cells were ever retrofitted with release locks in case guards needed to open them from the inside. Meanwhile, a slip of old-fashioned jargon alerts Rebecca to the fact that Donovan is not who he claims to be, and she draws her gun on him.
At that moment, the Ames brothers appear and start a shootout. Rebecca shoots Herman in the neck, wounding him severely, then Donovan attacks her and nearly overpowers her. When Herman dies, Pinky flies into a rage and starts shooting at Rebecca, but Hauser appears and fires back, holding off Pinky until Donovan grabs him, and the two flee into the prison halls. In the ensuing firefight, Hauser is shot in the side.
Pinky chases Hauser and Rebecca, but they escape behind a secure door into the control room. Despite Donovan's pleas to stick to their plan, Pinky insists on vengeance and plans to extract it against Doc. Meanwhile, Rebecca and Hauser try to determine exactly what the escapees' plan might be.
Chet finds the info Doc needs, and Doc is able to escape the cell, but he is immediately assaulted by the revenge-seeking Pinky. Before Pinky can permanently maim Doc, Donovan pulls a gun on him and forces him to stop, insisting that they use Doc as bait for Rebecca and Hauser.
While Hauser treats his own gunshot wound, Rebecca searches unsuccessfully to find a file on Donovan. The data on the Ames brothers reveal that they were high-risk, high-reward bank robbers who nearly pulled off a heist at a federal reserve, but there's nothing to indicate exactly what their scheme might be.
Hauser reasons that since the Ames brothers were often after federal gold, he thinks he knows what they were after: a rumored stash of Civil War gold held in secret at the prison, long thought to be an urban legend. Suddenly, Rebecca sees Pinky on the security monitor holding Doc hostage and promising to do to him what Rebecca did to Herman unless they turn themselves over to him in three minutes.
Rebecca tells Hauser that she'll turn herself over; she's counting on the fact that while Pinky wants blood, Donovan only wants gold. She plans to get Donovan to deliver Doc directly to Hauser. She asks if he's up for it; injecting himself with a painkiller, he replies, "No problem."
Back in '61, the Ames brothers follow their map through the tunnels under D block until they find a locked steel door to the "dungeon." Their keys don't fit the locks, and they realize that they need to race back to their cells, but they're surprised by Warden James, Tiller, and Ray, who hold them at gunpoint. James praises their daring but informs them that they took the wrong keys from him. He shows them the real key that opens the locks.
The brothers say that everyone knows the warden never lets the two keys they stole out of his sight. If they're not for the door to the gold, what do they open? "None of your damn business," replies James, who instructs Tiller to return the Ames brothers to the Hole, and he reminds the brothers that they each owe him a spoon.
James tells a puzzled Ray that he just helped thwart an ambitious escape attempt, but Ray thinks that they were only after what was behind the door. James tells Ray he's mistaken, and he offers him a commendation that "will put you in the history books" to avoid further misunderstanding. Ray accepts the commendation, along with the warden's offer to join him for dinner.
In the infirmary, Ray tells inmate - and his brother - Tommy Madsen that he's gotten an "in" with James. Rays asks him to trust him to learn what being done to Tommy.
In the present, Rebecca tells Donovan that she knows where the gold is and that Hauser will open the door for them if they release Doc. A cry from Doc alerts her to a sneak attack by Pinky, and she dodges his swing just in time. She's able to take Pinky down, but Donovan threatens to shoot Doc, so Rebecca runs away without her pistol. As Pinky stalks Rebecca in the cellblock, she lays a false trail and is able to kill him by dropping a steel bed frame on him from the second floor.
Hauser opens locked gates to allow Donovan and Doc to pass through on their way to the dungeon. Donovan wants to know where Hauser's hiding, but Doc insists that Hauser's "middle management, afraid of his own shadow." Donovan slams Doc against the wall and leaves him behind as he continues into the tunnels. Rebecca finds Doc, who is battered and bruised but still alive, and she thanks him for saving her life.
Donovan reaches the dungeon door, setting dynamite charges around it to blow it open, but Hauser appears with his gun leveled at Donovan. Hauser says that he was curious where Donovan thought the gold was, and Donovan says he knows its behind the door - he even offers to split the gold 50-50 with Hauser. When Hauser refuses, Donovan lights the fuses anyway.
Hauser is knocked senseless, but Donovan revives and pushes open the dungeon door. Rebecca arrives and corners a frustrated Donovan, who stands in the middle of a massive, empty vault filled with nothing but dust.
Later, Hauser tells a parable to the now-imprisoned Donovan at the secret prison facility as Dr. Beauregard prepares him for a procedure. Hauser recounts the story of an eagle who promises to deliver two men to a moon made of gold; when the men turn on each other and one ends up dead, the eagle eats the survivor in disgust. Hauser admits that while he knew about the keys, he didn't know that they belonged to the warden. He wants Donovan to tell him why everyone was so eager to learn what was happening to Tommy Madsen, and whether it's Warden James himself who's returned and masterminding the inmates' various sprees, hoping to reclaim the keys. "Take your time," he adds.
Back in '61, Warden James enters the dungeon by himself, walking past a cannon to a pull back a tarp, revealing a large stack of gold bricks. "Hello, ladies," he says with a grin.