At a country club fundraiser, Clarence Montgomery takes in the scenery, including a beautiful woman who's drawn to meet him when he steps outside onto a patio. After some initial flirting, the two commandeer a golf cart and set out on an impromptu late-night tour of the course. Making a stop in the midst of the links, Montgomery begins confusing the woman when he starts talking about the modest home he's bought for them, but she remains attracted to him.
As they lean in closer, Montgomery is suddenly stricken by a flashback featuring a similar-looking woman soaked in blood. Suddenly, Montgomery is in a panic, carrying across the golf course the limp, bloodied body of the woman he'd met. He sets her down on the green and methodically arranges her body into a specific position. He repeatedly asks the dead woman, "Who did this to you?"
The scene shifts to Alcatraz in 1960. In the prison kitchen, Warden James prepares a dish after summoning Montgomery; he offers the inmate a taste of his creation. After some prompting, Montgomery offers a detailed analysis of what the dish is lacking after just a quick taste, and the warden is pleased to get a demonstration of Montgomery's culinary gifts.
James offers him a position as head chef, which puzzles Montgomery. He expects that such a job would have to go to a white man, and he adds that the last time he cooked for white people it landed him in Alcatraz. The warden scoffs at his concerns, noting that it was taking knives to a woman's throat that brought Montgomery there. James offers the job as a chance for redemption, though he clearly has his own agenda at work as well.
In the present day, Doc uses the base computer to scan for crimes that might have been committed by the '63s, and he comes across the golf club homicide of a brunette woman in her early twenties. Upon closer inspection, the woman's body appears to have been arranged to identically match the position of Montgomery's first presumed victim in 1958, a detail Doc recognizes right away.
Montgomery visits his old prison friend Emmitt Little, who thought him dead and wants to know why he hasn't aged. However, it's another revelation that rivets him: under his overcoat, Montgomery is wearing a shirt covered in blood, and he claims to have killed a woman. Emmitt remembers that Montgomery was innocent of the original crime he was accused of, as Montgomery tries to explain that the experiments he underwent in Alcatraz had an effect on him and left him questioning his own innocence. Despite Emmitt's adamant reassurances, Montgomery protests, "I'm not innocent. Not no more."
In 1960, Lucy conducts a session with Montgomery, noting that he was the first black chef to serve in an all-white country club. Montgomery explains his belief that white people do whatever they chose, and that as a nonwhite even Lucy is subject to their whims - and their backlash.
In the present day, Rebecca, Doc, and Hauser investigate the golf course crime scene as Doc recounts Montgomery's history: After Montgomery fell in love with the daughter of the man who owned the country club where he worked, she ended up dead. The details of that crime match those of the current victim, a grad student who'd been killed elsewhere and moved to the 13th hole, just as had the original victim in 1958. The victim's friend can't identify Montgomery, telling Rebecca that she had a wild streak that caused her friends not to question her initial disappearance.
In 1960, Montgomery gets a shave while fretting to young Emmitt about the warden's job offer. Emmitt sees the opportunity as a symbol of progress and a chance to be an inspiration to others, but Montgomery just wants to serve his time; he believes that he can only be what whites tell him to be. Deputy Warden Tiller appears, taking issue with Warden James' attempts at rehabilitation and doubting the notion that the inmates can change - though he says that he's eager to see what happens next.
Consulting with her friend Nikki in the coroner's department, Rebecca explains that she's looking for similarities between the current murder and the '58 homicide. Nikki points out that a difference in the slashes on the victims' necks indicates that they were not killed by the same person. Doc appears and tentatively suggests that maybe the culprit's killing skills "improved," but Nikki demonstrates how the killers had to each favor a different hand: one was a righty and the other a lefty, meaning that the victims had different killers.
Rebecca and Doc gather Montgomery's belongings to search for additional clues, with Doc telling Hauser that whoever the culprit is, that person knows the Montgomery case intimately and has to be connected somehow. Still not fully convinced, Hauser gives them 12 hours to make progress in the case.
Along with prescriptions for penicillin and vitamin B-6 and recipes, Rebecca notices Emmitt's name circled in a batch of news clippings in Montgomery's file, and Doc recognizes Emmitt, who left Alcatraz in '61, as a major player in the Black Panther party. The pair track back to Emmitt's apartment, where he explains how while protesting during the civil rights movement he took a bullet to the back that left him confined to a wheelchair. Emmitt elaborates on Montgomery's innocence, telling Rebecca and Doc that Montgomery truly loved his girlfriend. When Rebecca asks if Emmitt knows if Montgomery was right- or left-handed, he claims his memory isn't what it used to be.
Nikki tells Rebecca she's found hairs from an African-American male on the victim's body that indicates Wilson's Disease. The illness causes the body to retain copper and results in an inability to move or think coherently without treatment - and the treatment explains the drugs in Montgomery's prison box. Rebecca believes that while Montgomery may have been innocent in the past, he isn't any longer.
Working as a caterer for an engagement party, Montgomery arrives at a posh job site, flashing back to his time in Alcatraz: He's accepted the warden's offer and heads the kitchen at the prison. When the warden compliments him on his soul food-style menu, Montgomery expresses his appreciation for the opportunity, realizing how much he's missed cooking.
In the mess hall, Warden James announces to the assembled prisoners that the meal is presented as their "parley," a civilized discussion under truce. But there's a rift brewing between the black and white inmates, and the whites reject the meal. A riot erupts, and the warden leaves Tiller, who's amused by the failure of James' efforts at race relations, to manage the fallout. Locked out of the kitchen, Montgomery is savagely beaten by a group of racist inmates until the guards gas the entire mess hall.
Back in the present, Montgomery oversees catering at the party until he's approached by a young woman strongly resembling the past victims. She flirts with him, and when she notes that the party is rather dull, he offers to take her on a walk.
After the woman turns up dead, the task force investigates the crime scene. Hauser is told by the police chief that there's a problem that needs to be discussed, but not on the site; Hauser agrees to meet him at a prearranged location. Meanwhile, Rebecca and Doc make the connection that Montgomery was part of the catering team when they recognize his recipes on the menu.
In 1960, Montgomery's cell is opened, and he's immediately punched by a guard and walked through a white cell block, where he's taunted by the inmates. He's then taken to a darkened room and strapped into an electric chair with his eyes taped open, while Dr. Beauregard administers an injection. A recording of the jury's guilty verdict from Montgomery's court case is played, and Beauregard rolls a film that intercuts the word "Guilty" with images of the first dead woman. Beauregard jolts Montgomery with 60 volts of electricity and leaves him to continue watching the film.
In the present, Rebecca tracks Montgomery back to the catering company and confronts him in the kitchen. He flees, and after an extended chase on the docks, he escapes after ducking under a passing semi truck and vanishing in the confusion.
Back in 1960, Tiller visits Montgomery as he works in the prison laundry. Tiller gloats that he was right that the prison wasn't ready for a chef like him. Tiller denies that his position is racist; he claims that he believes Montgomery and the inmates fail because they are criminals, not because they are "colored." Montgomery finds himself unable to rebut Tiller's assertion that he's a cold-blooded killer.
After Tiller leaves, Montgomery is joined by the talkative inmate William Gant, who compliments his cooking. Driven by the bloody images in his head, Montgomery finds himself compelled to pick up a box cutter and slash Gant's throat, killing him. Montgomery also begins to arrange Gant's body in the same position as the woman from 1958 before the guards discover him and drag him away.
In the present, after Nikki provides key info for tracking down where Montgomery is getting his modern-day meds, Doc casually suggests that he owes her a drink. He is flummoxed when Nikki appears to accept, and his awkwardness frustrates Rebecca.
The trail leads back to Emmitt, who holds them off with a shotgun. Now that the once-innocent Montgomery has been turned into a killing machine, Emmitt blames his imprisonment on Alcatraz. Meanwhile, in the rear of Emmitt's home, Hauser corners Montgomery, holding him at gunpoint through the window and insisting that they talk.
When Hauser agrees that Montgomery was innocent of the first murder in 1958, Montgomery admits that he did commit the modern-day killings. Hauser tells him that it has to end now. Montgomery confesses his crimes to Emmitt, explaining that he can't stop himself. He begs Emmitt to help him and keep them from putting him back in prison. After hesitating, Emmitt shoots Montgomery with his shotgun, killing him.
Hauser meets with the police chief, who is concerned that the task force's demand for secrecy is affecting the morale of his officers when they're not allowed close cases properly. Hauser gives the chief info that closes the original 1958 Montgomery murder case, providing him with the actual killer and proving Montgomery's innocence.
Rebecca and Doc are upset by the reality that while Montgomery was originally innocent, two girls are now dead due to his mysterious transformation into a killer. Doc surmises that Montgomery was the subject of one of any number of experiments conducted on prison inmates - experiments Doc didn't believe occurred at Alcatraz until now.
In 1960, Lucy again speaks with Montgomery, complimenting his culinary gifts after a sample. She's curious why he was trying to position William Gant's body to resemble the death pose of his girlfriend Ellen Casey. When he looks at photos of her, the images from Beauregard's film flash through his brain. Lucy suggests that his trauma is preventing him from moving forward, but he denies killing Ellen even as he admits killing Gant. She offers to help him by removing his memories, but he tells her she can't. He can't be stopped by her or anyone else.
Elsewhere, Warden James and Beauregard reflect on Montgomery's transformation from the only innocent in Alcatraz into a killer. Beauregard reminds the Warden that the experiment was done on James' order, and James admits the results lack elegance. Beauregard wonders exactly what the warden is having done to the prisoners' blood, but the Warden insists he's not doing anything, including keeping secrets from his staff.