Hauser and Ray meet after hours at Ray's bar. Ray wants Hauser to release Rebecca from the Alcatraz task force so she can have a normal life. Hauser says that it's not his decision to make. Unimpressed with the life Ray's made for himself, Hauser adds that he's glad Ray turned down his request to join the task force himself years earlier.
Hauser says that Ray doesn't have the stomach for the kind of work they're doing, and Rebecca does. Ray insists that Hauser cut Rebecca loose, but Hauser wants to know why Ray's waited months to make such a demand. Then Hauser realizes the answer: "Tommy Madsen - you've seen him."
As Rebecca sleeps, Tommy sits in a chair at the end of her bed watching her. Awakened by images of her previous partner's death while pursuing Tommy across a rooftop, Rebecca bolts up and aims her gun, but Tommy isn't there. Having apparently dreamed his presence, she gets up and goes over his file yet again.
Two wealthy men banter as they drive through the night in a luxury car, until they nearly hit a man in the road. As they pull over to investigate and find no one there, former Alcatraz inmate Sonny Burnett appears with a cocked shotgun. When one of the men tells Burnett he can take anything he wants, Burnett says, "OK," and casually shoots him. "I'll be taking you," Burnett tells the other man.
In 1960 Burnett is released from his initial 30-day stint in solitary as a new inmate to be placed in the general Alcatraz population. In the recreation yard, Burnett asks fellow inmate Boyd Hicks for protection, but Hicks rebuffs the offer, suggesting that no one is protected in Alcatraz - he merely provides "a deterrent." Burnett persists, explaining that he has considerable money from his crimes as a kidnapper to pay, and he needs protection during his entire stay in Alcatraz. "They caught up with me, not the money," he explains.
Back in the present, they arrive at the crime scene, and Rebecca tells Doc that her dream about Tommy has been a recurring one. Hauser shows them Burnett's Alcatraz inmate uniform and reveals that the kidnapping victim is David Pierce, the CFO of the multimillion dollar firm Helen Campbell Cosmetics. He's also the founder's husband.
Doc points out that in the 1950s Burnett ran his successful kidnapping and ransom schemes like a business. He always returned the victims unharmed once he'd been paid, unlike the current murder or Pierce's colleague. Rebecca urges Hauser to sit this one out after being shot during the Ames brothers case, but he refuses.
Later, while interviewing Pierce's wife, Helen Campbell, Rebecca tells her that they expect that the abduction is about money. Then Helen surprises her by revealing that she, too, was kidnapped when she was a child - by Sonny Burnett.
As Dr. Beauregard tends to Hauser's gunshot wound, he points out that wounded Alcatraz escapee Ernest Cobb's own wound healed at an accelerated rate, and that all the returned '63s are in remarkably perfect health: previous ailments have vanished, and their blood work reveals the presence of colloidal silver, an ancient healing element. Beauregard also not-so-subtly suggests that a blood transfusion might transfer those healing properties to another body, but thus far none of the recaptured inmates share a certain "good doctor's" blood type for experimentation. "Not yet," Hauser says.
Helen explains to Doc that because she was a minor when she was abducted, her name was withheld in all of Sonny Burnett's reports, which is why Doc wasn't familiar with her case. As Rebecca says that revealing the details of Helen's kidnapping might help them in recovering her husband, Hauser arrives and suggests that the current case could be a copycat of Helen's childhood trauma.
Helen was living on her own at age 14, and Sonny recruited her as an accomplice into his kidnapping schemes, apparently through intimidation. When she finally worked up the courage to break away from him three months later, she went to the police, and Burnett was arrested.
Rebecca wants to know where he kept her prisoner. Helen's hesitation makes it obvious that she's holding back information. Hauser takes Rebecca aside and cautions her not to push too hard or Helen will cease to cooperate at all.
Ray visits Rebecca at her apartment, telling her that he's under surveillance by Hauser's people. Rebecca wonders if Hauser expects Tommy to make contact with Ray, and Ray denies seeing him. Ray is concerned when he finds Tommy's file open on Rebecca's desk, and she reveals her history with Tommy on the rooftop when her partner died.
Now she wonders why it seemed like there was some personal vendetta between Tommy and her partner. Ray denies any knowledge, and Rebecca tells him that she wishes she could believe him. "What is it about Alcatraz that makes everyone turn into a liar?" she asks, suspecting that Ray has indeed had contact with Tommy.
Back in 1960, Hicks tells Burnett that when his minions on the outside of the prison went to retrieve Burnett's cash, the box he said it would be in was empty. Burnett is shocked to hear the news, believing that no one else knew where he hid the cash. As payback for wasting his time, Hicks shanks Burnett in the prison yard.
In the present day, the bound David Pierce tells Burnett to call his wife. He says that she'll give him anything he wants. Burnett laughs in David's face.
In the past, Burnett wakes up in the infirmary, tended to by Dr. Beauregard - who informs him that he had clinically died for 30 seconds - as Warden James and Tiller look on. Burnett tells them that he just wants to serve his time in peace, which amuses Beauregard, but the warden wants to put him back into the general population.
Tiller disagrees, but James insists that survival and natural selection overrule all things at Alcatraz and that Tiller "of all people" should understand knowing one's place in the food chain. Tiller tells Burnett that there's no such thing as doing time in peace. He suggests that Burnett should choose which he wants to be: predator or prey.
Hauser and the task force play Burnett's ransom call for Helen. She's revealed that the money drop location - a horse racing track - is the same place she was held and escaped from as a girl and that the $100,000 demand matches Burnett's last ransom request. Rebecca goes to the track to make the drop.
Meanwhile, Burnett kills the police officers guarding Helen's house, and he confronts his former victim within. Helen is shocked to see the un-aged Burnett, especially after being told that he had died.
He accuses her of betraying him and taking his money after she told him she loved him. She responds that she was only 14 and did whatever he said. Burnett wants to make her feel the same pain of losing everything that he felt. He tells her that David is in the stable where he sent the task force - "at least part of him" is there. Just then, Rebecca discovers David's severed head at the racetrack.
Reasoning that Burnett's prime motivation is to make Helen, whom he's left alive and unharmed, suffer now, the task force decides to put police protection on anyone who's significant to her. Forensic scientist Nikki tells the task force that Burnett used a power saw to behead David, and she urges Rebecca to either catch or kill Burnett. Doc agrees that it might be better not to take Burnett alive, but Hauser insists that all the Alcatraz inmates be brought in for imprisonment. "He does realize he's the only one who shoots them, right?" Doc asks Rebecca.
Shocked that Burnett had not aged, Helen realizes that Hauser knew all along that her kidnapper had returned somehow, and she demands answers. Rebecca insists that Helen reveal the reason for Burnett's personal vendetta against her.
Helen explains that the night before she escaped, a drunken Burnett said where he hid his ransom money, telling her that she was the only one he trusted. Once he'd been captured, she scoured the location for two weeks until she found the money, believing she deserved it for what Burnett had done to her.
She breaks down, blaming herself for her husband's fate, and she wonders if Burnett will always be out there threatening to murder her loved ones. Moved by Helen's fears, Rebecca tells Hauser that Ray thinks he's having him watched. Hauser asks if she wants him to back off, but Rebecca says she wants to be the first one called if Tommy shows up.
When Doc develops a lead on Burnett based on his penchant for flashy muscle cars, he and Rebecca head out to investigate. Arriving at his hideout, Burnett flashes back to 1960, remembering how he relentlessly trained himself physically to survive his incarceration.
In the prison yard, Burnett gets into a violent altercation over virtually nothing, viciously beating another inmate - one of Hicks' underlings. Hicks promises payback after Burnett is released from solitary.
Checking out Burnett's hideout, Rebecca finds the power saw used to kill David as well as evidence that Burnett has the number of an arriving flight carrying Helen's daughter, Danielle.
Posing as a limo driver at the airport, Burnett tricks Danielle into coming with him. Later, at a hardware store, Burnett purchases a new blade for his saw, several pieces of plywood cut to the height of a person, and a flashlight.
Back in 1960, Tiller delivers a hearty meal to Burnett's cell, and he openly admires the fire within Burnett that's motivating him to adapt and move further up the food chain. Tiller suspects the reason is Helen, as her name was Burnett's last word when his heart briefly stopped: "A man's dying words carry the weight or either love or loss - usually both," says Tiller, pushing Burnett further by expressing his disappointment that Burnett didn't see his beating of the convict all the way through - to death.
Burnett's trail leads Rebecca and Doc to the hardware store, where they realize that he has buried Danielle alive, most likely in the same field where he previously stashed his ransom payments. At that moment, Burnett finishes shoveling dirt over the buried Danielle and is about to leave, but Hauser has tracked the stolen limo's LoJack signal to the field, and Rebecca and Doc arrive just in time to pursue Burnett.
Back in the prison yard in 1960, when Hicks confronts Burnett upon his release from solitary, Burnett launches into a no-holds-barred assault, ultimately gouging Hicks' eyes out as Tiller watches. Warden James remarks on Burnett's transformation but wonders why he didn't kill Hicks to extract his revenge. Tiller points out that what Burnett did was worse. As Tiller gloats, James cautions him to remember whose wolf pack he is part of.
In the present, a police barricade and a barrage of bullets halt Burnett's escape, then officers wrestle him into handcuffs. Hauser claims federal authority over him, but the ranking officer wants custody because Burnett killed two of his men. However, when Rebecca explains that Burnett buried a woman alive in the field, the officer cooperates and calls in reinforcements to search for Danielle. Eventually, the rescue crew unearths Danielle.
Later, as paramedics tend to her daughter, Helen reflects on how one decision 50 years earlier led to everything that happened. She believed that Burnett was out of her life forever; Rebecca promises her that he is at last.
Rebecca tells Doc that Hauser has Ray under surveillance in hopes that Ray will lead him Tommy. Doc is surprised when Rebecca reveals that she's OK with Hauser's tactic. He reminds her that one day, when all this is over, the three of them will have to live with everything that they've done.
At the bedside of the still-comatose Lucy, Dr. Beauregard tells Hauser that while Burnett's blood type matches Lucy's, there's no evidence of colloidal silver in his bloodstream that might be used to heal her. Hauser is frustrated, and Beauregard reminds him that not of all the 300 inmates were "taken an interest in." Hauser tells Beauregard to walk away. Meanwhile, as Rebecca sleeps, the real Tommy Madsen peers in his granddaughter's window.