In 1963 young police officer Emerson Hauser battles seasickness on the ferry to deliver inmate Paxton Petty to Alcatraz Island. They are greeted by an unusually large welcoming party, including Warden James, E.B. Tiller, and Lucy Sengupta.
Petty's criminal history includes setting hidden mines that have hurt and killed families, and the warden warns him that the Alcatraz team will do whatever's necessary to learn if there are any undiscovered mines left to be tripped. As the group disperses, Hauser awkwardly offers Lucy a ride back to the mainland. She politely declines, offering him a mint to ease his stomach, and the two appear to share a moment.
Time shifts to the present day, as Hauser continues his vigil at the bedside of the comatose Lucy, with Billie Holiday's "These Foolish Things (Remind Me of You)" playing in the background. Lucy's doctor tells Hauser that she's not showing any improvement, and he delicately inquires whether Lucy had previously indicated that she has a "Do Not Resuscitate" plan. Hauser infers that Lucy is likely dying.
At a San Francisco dog park, dog owners and their pets unexpectedly trip land mines that explode violently, leaving the park littered with casualties. Hauser, Rebecca and Doc investigate the scene - which is also observed by Paxton Petty, who blends into the crowd as a bystander but is noticed by Rebecca.
Doc and Hauser instantly recognize the mines as Petty's handiwork and recount his history for Rebecca: Petty previously set up three minefields in the city and claimed that there was a fourth, but it was never found. He was a former solider suspected of killing school children with mines in the Korean War; he was subsequently court-martialed and put on graveyard duty at the Presidio until he was convicted and sentenced to six years in prison. Upon his discharge, Petty unleashed his reign of terror on San Francisco until he was caught and imprisoned in Alcatraz.
When Doc shows Rebecca a newspaper photo of Petty on his iPad, she recognizes him from the crowd and spots him walking away smugly. She pursues and draws her weapon, but he rolls a mine in her direction that destroys a car as she ducks for cover. In the aftermath of the explosion, Petty has vanished.
Rebecca wonders where Petty is getting the mines. Doc theorizes that whoever provided the other Alcatraz inmates with their weapons of choice may be responsible for helping Petty. Rebecca spots an old friend from the bomb squad, Matt Tanner, who tells her that the bombs seem to be older models modified to blow various shrapnel to maximize the carnage.
Rebecca and Doc visit her friend Nikki in the medical examiner's office. Doc is smitten when she takes off her scrubs to reveal a Golden Age Sandman t-shirt. Nikki discovers that the shrapnel appears to include broken bits of military medals.
On Alcatraz, Hauser sorts through his old belongings, discovering a yellowed photo of himself and Lucy. He finds Petty's file, which includes a handwritten note, apparently song lyrics, with the words "snow," "beard," and "grace" circled.
The scene shifts to the '60s, where Dr. Beauregard tries to extract the fourth bomb location from Petty by dunking his head underwater. Lucy is disgusted by the method, but Warden James endorses a mix of Lucy and Beauregard's techniques to achieve the desired results. Still, when she continues to object, James lets her see Petty's next round of questioning.
In the present, Doc notes that Petty believed he deserved a medal, firing off angry letters during his incarceration demanding a Silver Star - the same kind of medal making up much of the shrapnel. Because such medals are rare and treasured by the military and their families, most are buried with the recipients. This leads Rebecca to believe that Petty's supply came from the graveyard at the Presidio during his service there.
Meanwhile, hiding inside a crypt, Petty is altering more medals for his mines. He's surprised when he's discovered by a security guard. Petty kills the guard.
A Presidio caretaker points Rebecca and Doc to a corner of the cemetery where Petty may have found the medals he gathered, but the grounds appear untouched. Rebecca realizes that Petty may have hidden his stash somewhere no one had looked throughout the intervening decades. She investigates a nearby crypt.
In the 60s, Lucy tries to get Petty to open up, revealing that she drugged the tea she's given him with a mild sedative designed to make him relax. Petty tries to resist speaking with her, but she recounts his service history: he lived through a battle in which several survivors were granted Silver Stars but not him, despite clearing several frozen minefields on his own. As Lucy paints a sympathetic portrait of Petty's experiences and why he might have begun to see civilian children as the enemy in Korea, she subtly hooks him up to an electroshock device and applies a charge. After the voltage is administered, a dazed Petty sings a mysterious song to himself in Korean.
Lucy later plays a tape of the song back to inmate Tommy Madsen. As a veteran himself, he might recognize the significance of the song. Madsen tells her that he'll only cooperate if she will reveal why he's constantly in the infirmary and having blood taken and tested when he appears to be perfectly healthy. Lucy agrees, and Madsen reveals that the tune is a Korean lullaby: the lullaby was a coded way for the Korean soldiers to recall where land mines were placed, with each verse featuring key words to indicate specific locations.
Back in the present, Hauser continues to study the circled words, aware of their significance: they correspond with the locations of Petty's mine attacks in the '60s. Online, he discovers a second verse to the song and begins matching words to Petty's modern day attack.
Meanwhile, Rebecca and Doc realize that Petty broke out of - rather than into - the crypt, suggesting that it was his arrival point in the modern day after vanishing in '63. They discover his long-hidden stash of weaponry and shrapnel. They realize from his other tools that he's specifically planning to hide his mines underneath children's playgrounds. He could strike at any school or park in San Francisco.
After Rebecca shares the details of her investigation with Hauser, he demands that she cross-reference the potential mine locations with the word "windward." As Rebecca and Doc discover a single locale with the keyword - an elementary school - Hauser also computer-searches locations based on another word he's decoded from the lyrics: "sunset."
At Windward Elementary, Tanner tells Rebecca that the grounds appear clear. She calls Hauser, who arrives at Sunset Beach and tells her not to move. Hauser discovers Petty digging in the beach sand and holds him at gunpoint. Walking toward Petty, Hauser hears a click and realizes that he's just depressed the trigger on a mine. Petty pulls his own weapon on Hauser and demands his gun and phone.
After sundown, Rebecca and Doc stake out the school and spot Petty preparing to hide his mines on the playground. Rebecca draws her gun on him, and Petty wonders if she's working with Hauser. She kicks him to the ground and cuffs him, then tries to call Hauser only to hear Hauser's cell phone ringing from within Petty's backpack. She demands to know where Hauser is, but Petty simply responds, "Tick, tick, tick . . ."
With Petty behind bars, Rebecca tries to learn what's happened to Hauser. Petty suggests that he's probably dead by now - and Petty has some questions of his own. He wants to know what happened to him and how he went to bed what feels like a week ago only to wake up inside a tomb.
Rebecca leaves Doc to talk theories with Petty as she searches the Alcatraz computer lab for clues. She discovers that Hauser was the cop on Petty's case back in the '60s. Finding Hauser's lyric sheet, she zeroes in on the "sunset" location.
When Doc reveals to Petty that he never wrote about him in his Alcatraz books, Petty is annoyed - he believes he was important, based on what the warden and "the lady head-shrinker" told him. Doc is surprised at the reference, having never learned of any female doctors working at the prison. Then, having reasoned out Hauser's location, Rebecca drags Petty along with her as she rushes to save him.
In the '60s, Lucy puzzles out Petty's lullaby lyric code, telling Warden James that the fourth bomb is hidden at a location tied to the words "Twin Tree." She doesn't get the reference, but she's already alerted the San Francisco police. The warden is pleased at the credit Alcatraz will receive. When she has a moment alone with Dr. Beauregard, Lucy questions him about the constant medical treatment Tommy Madsen's been subjected to when he shows no verifiable illness. Beauregard warns her not to overstep her boundaries.
Rebecca, Doc, and Petty arrive at the beach to find Hauser still standing on the land mine. After Rebecca calls in the bomb squad, Matt works to disarm the mine. He's forced to improvise due to Petty's modifications, while Hauser reveals that he never found the bomb hidden with the "Twin Tree" clue - he's been looking all these years after promising a friend he'd find it. Matt thinks that he can beat Petty's reworking on the mine and wants Hauser to step off the plunger so he can defuse the mine.Rebecca helps Hauser get away from the mine, and Matt works quickly to deactivate it. But Petty's rewiring fools him, and Matt is killed when the mine explodes unexpectedly. Furious, Hauser delivers payback to Petty, shooting him in the leg and telling him that all his schemes have reached the end. He claims that the "Twin Tree" bomb went off 20 years earlier and didn't harm a soul.
Petty insists that the nature trail he planted the bomb on was too heavily trafficked not to have harmed someone. Hauser informs him that the location had been sold the state and shut down - but he thanks Petty for revealing where they should look for the mine. Hauser holds his weapon to Petty's head and considers shooting him a moment, worrying Rebecca and Doc, but he lowers the gun and walks off.
In the '60s, Lucy visits Hauser at the police station and asks if he's found the "Twin Tree" location. After some banter, the two plan to go out to dinner together.
In the present day, Hauser tells the comatose Lucy that he found Petty's final bomb, delivering the defused component to her bedside. Hauser detaches the life support equipment from Lucy and gathers her up in his arms. When the nurse comes into the hospital room to investigate, they've both disappeared. Hauser carries Lucy into the secret prison facility, where he tells Dr. Beauregard, "You know her methods - fix her!"