The scene opens in 1960 in Alcatraz, a young Emerson Hauser vomits over the side of a boat in the Alcatraz dock, as Lucy and Warden James arrive to receive a new prisoner Paxton Petty, notorious for planting mines in populated areas in San Francisco, and thus a dangerous criminal; one deserving of a facility like Alcatraz. Warden James assures Paxton that they’ll find his remaining mines by any means necessary, but before they head into the prison Hauser nervously asks if Lucy needs a ride to the mainland. She declines, but offers him a peppermint for his nausea; thus begins a beautiful friendship. In the present, the elder Hauser watches over Lucy’s unconscious body, playing music for her, when a doctor arrives to report that she’s shown no improvement; much to Hauser’s dismay, and may need DNR instructions.
Hauser is as usual, visibly worried and disturbed by her condition. Somewhere at a local park, a man looses a dog to go for a run, when suddenly a mine beneath him explodes and blows off his leg, truly gruesome visual. Multiple mines erupt nearby, injuring other pedestrians, and in the process causing utter chaos and confusion. When Rebecca and Diego arrive on the scene, Rebecca notices a suspicious man at the scene that we know to be Paxton; as is show earlier, while Hauser and Diego figure out on their own that the incident is his handiwork; based on the pattern of the crime, describing him as a combat engineer eventually tried for war crimes.
When Madsen sees his picture, she takes off after the man from earlier and stops him; as she recognizes the man she had seen earlier, from the picture, and owing to the fact that he still looks the same, but in defense he rolls a mine at her; in order to lose her, she barely escapes his attack. They lose his trail in the bargain. After recovering, and barely escaping with her life, Madsen notices a friend among the bomb squad, in the form of Matt Tanner. They note that some of the shrapnel contains rather uniquely-shaped metals, which a visit to Madsen’s medical examiner friend (whom Diego attempts to hit on) reveals them to be pieces of war medals; a truly strange discovery. Meanwhile, on Alcatraz, Hauser examines some of his old possessions, including photos of him and Lucy, and song lyrics with the words "brooke," "beard" and "grace" circled; he is probably nostalgic, or looking at the circled words, probably on to something, just then we flash back to Paxton Petty’s torture via ice tub, back in the Alcatraz of 1960.
He still refuses to divulge the location of his mines, and Lucy insists that they need to try psychological methods instead; because conventional methods do not seem to be working on him, and getting the information out of him quickly is imperative, as time is of the essence, especially as many lives are at stake. Meanwhile in the present, having learned that the medals are in fact silver stars, Rebecca and Diego figure out that the only place to get those would be off of exhumed soldiers from Paxton’s graveyard shift at the Presidio. They arrive but find no undisturbed graves; leaving them stumped, but Rebecca eventually realizes he’d have to hide them where no one would look, so as to not raise any suspicions.
Meanwhile back in the Alcatraz of 1960, in Lucy’s old office, she serves Paxton tea to warm him up; or so it seems, before revealing that she in fact drugged the tea to make him more docile; thus safeguarding herself and as a precaution against any aggression from his end, along with making him more receptive to her line of questioning. She questions him about his time in the war, all-the-while setting him up for electro-shock therapy. Post the electro-shock being administered, Paxton starts humming a tune. She seeks out Tommy Madsen for the meaning of the tune, which in exchange for her finding answers of why he’s kept in the infirmary for his blood, confesses that the song represents a pattern to remember where mines are stashed. Thus her methods seem to have made headway, in acquiring some information; just as she had predicted, they would.
In the present, Rebecca and Diego enter the Mausoleum finding Paxton’s stash of mines recently painted to resemble playground colors. She calls Hauser to update him on the situation, when he demands she cross reference her results with anything “Windward,” though they find nothing at the local Windward Elementary School Park. Hauser meanwhile goes off on his own to another of Paxton’s targets, a Sunset beach, accidentally stumbling on Petty planting his mines. Before he can apprehend him, he steps on one of the mines, and is forced to remain in place for the time being; as he has no wish to be blown to smithereens. Later that night while staking out Windward, Paxton arrives to plant his mines and Rebecca subdues him, but realizes that he’s done something with Hauser.
Rebecca throws him in his cell in present Alcatraz, and Paxton insists that he wants to know why he awoke in the year 2012 in a graveyard; he is completely baffled by this phenomenon. Rebecca leaves Diego to entertain Paxton with his theories on the time jump, and uncovers Hauser’s research of the song lyrics, leading her to put together his location at Sunset beach. She lets Paxton out and drags him to the beach, but not before he mentions something to Diego about an unrecorded female doctor in Alcatraz’s past. Speaking of the past, Lucy informs Warden James of the methodology for finding the mines, but Dr. Beauregard refuses to answer any of her questions about why Tommy Madsen is being kept in the infirmary. Back in the present, Rebecca calls the bomb squad to help free Hauser from his predicament, despite Paxton’s taunts; that they won’t be able to manage saving Hauser.
Tanner reveals that Paxton wired this mine specially to be difficult to diffuse, and while a momentary respite allows Hauser to escape unharmed, the mine still detonates; despite their best efforts in preventing that from happening; unfortunately killing Tanner. This angers Hauser to no end. Hauser shoots Paxton in the leg and deceives him by saying the missing mine from 1960 blew up twenty years ago. When Paxton reacts, he inadvertently reveals the real location, and Hauser thanks him for instructions on where to dig. Thus leaving Paxton, feeling like a fool. In the past, Lucy arrives at Hauser’s work station to ask about the “Twintree” outlined in Paxton’s notes, but also offers him a chance to take her to dinner; a proposition that visibly gladdens Hauser.
In the present however, aged Hauser whispers to a comatose Lucy that he finally found the mine, before unhooking her from life support and carrying her out of the building. He takes her all the way to New Alcatraz, where he commands Dr. Beauregard to “fix her” using her own methods. Possibly because, he no more has faith in conventional medical procedures, and thus wants the doctor to try something unconventional in order to revive her. The episode ends.