In a dilapidated apartment on Alcatraz Island, a clean-cut man quietly surveys the rundown environment, prying open a hidden compartment at the base of one of the walls and gazing nostalgically at the faded black-and-white photos stashed within: images of the man and his family.
His reverie is interrupted by an Alcatraz park ranger who tells him that he doesn't belong there. The man savagely attacks the ranger, beating him unconscious. He stuffs the photos in his pocket and retrieves one more hidden item: a handgun. He pauses on his way out, staring at a doorframe marked at different points in pencil with a child's height. The memory causes the man's mind to wander into a flashback.
In 1960, the man's wife awakens to find him dressed and ready to leave their house as he admits to being too excited to sleep. He resists his wife's playful suggestion to call in sick - "It's training day," he reminds her - and even his young daughter, whose growth is charted on the door, can't tempt him to skip work and stay home with his happy family.
At Alcatraz, the man, who is revealed to be prison guard Guy Hastings, addresses his rookie officers in the pouring rain. He stresses that no single man can go it alone on Alcatraz. The recruits then sound off, including Ray Archer, Rebecca's adoptive uncle.
Over Chinese food in the present day, Ray shows Rebecca an old photo of himself as a young boy with her grandfather Tommy; he says that they knew each other long before they worked together at Alcatraz. Rebecca asks if Tommy really killed his wife, her grandmother. Ray responds that he didn't think so at first - and then he did.
Rebecca is called to the task force headquarters, where Hauser shows her footage of Hastings' assault on the ranger. Because the guards were good men, Hauser believes that someone put Hastings up to the attack: most likely whoever took the missing '63s. Meanwhile, Hastings watches Ray from outside his bar.
As the task force investigates Hastings' old apartment on Alcatraz, Doc reviews the guard's background. Hastings was a former Navy man who came to the Rock with his family in 1957. He supposedly died with five other guards in a chemical spill in 1963. Doc comes to the realization that much of the information in his books is fraudulent. They discover Hastings' secret hiding place, and when Rebecca wonders how they'll ever track him, Doc suggests that they find his daughter, Annie.
Having located Annie, Doc and Rebecca approach her, claiming that Doc is writing a new book and Rebecca is his research assistant. Annie, who was eight years old when her father "died," remembers Alcatraz as an amazing place to live, one where here parents never locked their doors. She recalls the last time she saw her father on the day of the alleged accident. She and her mother were sent back to shore and later told of his death, although they never received a full explanation of what exactly happened. Annie allows Doc to take a box containing her father's possessions.
In 1960, Hastings shows the new guards the Alcatraz mess hall, known as "the gas chamber" because of the 14 tear gas canisters affixed to the ceiling. It's the most dangerous room in the most dangerous prison in the world. Hastings tells the guards that they'll need eyes in the back of their heads to stay safe, making his point clear to young Ray.
Suddenly, inmate Tommy Madsen catches sight of Ray, who smiles at him. Tommy assaults Ray with his dinner tray, telling him that he shouldn't have come there. Hastings breaks up the fight and orders Madsen confined to the "Hole."
In the present day, as Ray takes out the garbage at his bar, Hastings confronts him in the alley, holding his gun on him. As he turns to look at Hastings, Ray is shocked to recognize him from the past. Hastings knocks him unconscious with the butt of his weapon.
In the past, Dr. Beauregard stitches up young Ray's head wound, admitting that he forgot the anesthesia because he doesn't usually bother. He notes that the deep cut suggests his assailant had "a real itching for you." Warden James and Tiller arrive, and the warden is irritated to have his family time interrupted for a seemingly inconsequential assault. Beauregard says that he only called for Tiller as regulations require. Tiller brought the warden because he finds the incident extremely strange, but James says that on Alcatraz, "Strange went out the window" the moment anyone set foot in the island.
Tiller suspects young Ray of being planted there to break Madsen out. After Ray insists that he's still got the courage to continue his detail on Alcatraz, James leaves the decision to Hastings. Though green, Ray's shown his willingness to stay when other men would bolt, and Hastings says he deserves another shot. James is satisfied but says that any further incidents involving Ray will be on Hastings' head.
In the present, Doc only finds medals and Navy memorabilia - "good guy stuff" - among Hastings' effects, providing few clues. Then Ray's employee J.T. calls Rebecca to tell her that Ray disappeared after leaving to take out the trash. Hauser mysteriously agrees to join Rebecca as she leaves to investigate, and before they exit Doc discovers a photo of Hastings and Ray together at Alcatraz.
Ray awakens, handcuffed, to see Hastings rifling through his apartment, searching for something. Confused, Ray asks how Hastings is still alive, but Hastings doesn't explain - instead he demands to know where Tommy Madsen is. Ray claims that he only knows Tommy as an inmate, the same as Hastings, but Hastings insists that Ray's lying. As Ray wonders why Hastings still looks the same as he did in the '60s, Hastings studies Ray's photographs and comments that Ray got to live a whole life and raise a family - he assumes from a photo of Rebecca that she's Ray's daughter.
Seeing a photo of the young Ray together with Tommy Madsen, Hastings shoves it in Ray's face as proof of their connection. Ray tells him that Tommy died in 1964, but Hastings knows differently: "Same as I'm here, so's he." He wants to be taken to Madsen's son, and when Ray tries to tell him that he can't, Hastings levels his gun at Ray and insists.
Rebecca and Hauser arrive at Ray's apartment, but Hastings and Ray are gone. Finding a watch that she bought Ray when she was 13, Rebecca believes that Ray's trying to send her a message by leaving it behind. She wonders why Hastings would target Ray, who left Alcatraz before the incident that closed it down. When Hauser finds the shattered photo of young Ray and Tommy, he suggests that Hastings is really after someone else: her grandfather.
In 1960, after having put himself on the line for Ray, Hastings asks him one time for a straight answer: Does he know Tommy Madsen? Ray says firmly that he doesn't. If that's the truth, says Hastings, Ray has another problem. Respect is the key currency on Alcatraz, and 100 inmates saw Madsen split Ray's head open. Hastings suggests that for his own safety, Ray needs to prove himself and show that he doesn't know Madsen by making an example.
In the present, after Rebecca and Doc notice that Hauser has behaved with an especially mysterious tact with this case, Doc discovers that Hastings was Ray's training officer and that Madsen attacked Ray in his first week on the job.
Rebecca tries to recall the familiar home in the photograph as they piece the clues together. It stands to reason that Hastings is forcing Ray to take him to the house where Tommy grew up, and they just need to identify its location. Doc wants use a computer model to build out the image of the home; they might be able to determine its neighborhood from the architecture, but he needs to call in a professional to help.
Ray has taken Hastings to Tommy's son's grave to prove to him that everyone connected to Tommy is dead except Ray. Knowing that Hastings never wanted to hurt anybody, Ray asks why he's so fiercely on Tommy's trail.
"It's what they told me," replies Hastings, expecting Ray to remember what was being done to Tommy and why he frequently spent weeks in the prison infirmary - Hastings assumes that's why Ray left. "I left to raise his son," Ray tells him.
Hastings notices that Tommy's son's grave is inscribed, "Beloved husband and father," and he realizes that Rebecca, whom he saw in Ray's photos, is too young to be Ray's daughter and has to be Tommy's granddaughter. Ray tells him to leave Rebecca out of it, but Hastings thinks that she might know where Tommy is. To protect Rebecca, Ray agrees to take Hastings to Tommy.
In the present day, Rebecca wonders about Doc's choice of a "pro" - his comic book store stock boy Chet - but Chet comes through, using CG imagery to determine a likely location. Doc then uses 1950s census data to try to target the neighboring Madsen and Archer homes.
Meanwhile, Hauser quizzes the consultants from his think tank, wondering if seismic activity had any connection to the '63s time jump. He then focuses on why a guard like Hastings is specifically after Madsen: they believe Madsen has been lost by those responsible for the '63's disappearance.
As Rebecca and Doc scan the records with no sign of an "Archer" family near the Madsens they've discovered, Rebecca makes a startling find when she takes a closer look: Ray is actually Tommy's younger brother. He changed his name to get the job on Alcatraz, and he is Rebecca's grand-uncle.
In 1960, Hastings and young Ray prepare to enact their plan as the inmates are lined up to be reinstalled in their cells after a meal. Ray opens and closes all the cell doors except one: Tommy's. With Tommy left standing in front of all the other inmates, they begin chanting for a fight as Ray approaches him and orders him into his cell. Ray bashes Tommy's head against the bars and beats him senseless until Hastings pulls him away.
In the present, Ray brings Hastings to Tommy's childhood home. "If there's any place Tommy'd go," Ray says, "it'd be here." Rushing to the same location, Rebecca and Doc are surprised to get a call from Hauser, who knows where they are. Doc wonders how Rebecca will handle any encounter with Tommy. He may have caused her partner's death, but he's also still her grandfather.Ray recalls his first day at Alcatraz, when he was so scared that the only thing that kept him from bolting back home was Hastings. Ray wants to know what happened to Hastings and where he's been. "I haven't been anywhere," Hastings replies. He'd sent his daughter off to school and worked in the guard tower at night until "the fog took the stars away." Then he'd awakened in the infirmary and was told that there'd been an accident. Most of the guards were there with him; they were informed that their families had been killed and that they were all sick and contaminated, unable to be released. And suddenly, "It wasn't 1963 anymore."
Hastings is alerted by Rebecca and Doc's arrival. Despite Ray's warning, Hastings gets the drop on Rebecca, capturing her. Rebecca tells Hastings that she knows he's a good man, and that his daughter Annie is still alive. He doubts her, but when she reveals personal details that Annie shared with her, he wavers.
Hauser arrives and draws a bead on Hastings, telling him that he'll shoot him in the head on the count of three - even though Ray warns him he doesn't have the shot. Trying to spare Hastings, Rebecca manages to break his hold and shoot him in the leg, disabling him and keeping Hauser from killing him.
In 1960, young Ray visits Tommy in the prison infirmary. He tells his brother that he knows he's not wanted there, and it doesn't matter that Tommy believes he deserves his imprisonment, because Ray believes he does not. Ray won't leave him to rot in Alcatraz by himself - they're in it together. As Ray turns to leave, Tommy grabs his hand.
As Hauser prepares to take Hastings into custody, the guard asks Rebecca if what she said about Annie still being alive is true. "Alive, and with great memories of her daddy," replies Rebecca. Later, Hauser parks his SUV across from Annie's home and allows Hastings to see her with her children and grandchildren. Overwhelmed by how happy his family looks, Hastings asks Hauser why he allowed him to see them, and Hauser tells him he's a casualty of the Alcatraz situation, and he didn't deserve what has happened to him.
"I'm never going to see them again, am I?" Hastings asks. "No," replies Hauser.
After silently watching Ray inside his bar, Rebecca approaches Hauser in the task force HQ: "I'm not the first Madsen you asked to be part of this task force, am I?" She's reasoned that Ray hasn't freaked out about Hastings' appearance because he'd already been clued in about the Alcatraz situation, and Hauser thought Ray would have known how to find Tommy.
Hauser admits offering Ray a job 16 years earlier but says that Ray turned him down to focus on raising Rebecca. She confidently points out that now she knows because of her personal connection to Tommy, Hauser needs her more than she needs him.
Alone in his bar, Ray is surprised when Tommy appears - Ray told him never to come there. Tommy says that with their childhood house revealed he has to find a new place to hide. Tommy remembers when Ray would've done anything to protect him. That was before Rebecca, Ray tells him. Tommy is amused to think of himself as a grandfather, but Ray responds adamantly: "You're nobody's grandfather."
Ray orders Tommy to "get the hell out of my bar." Tommy agrees to go but says it isn't over. Ray informs him that every moment Tommy is near, Rebecca is in harm's way, warning him, "If I see you again, I'll kill you."