In 1960, Ernest Cobb is brought into Alcatraz for the first time, paraded naked down the cell block by deputy warden Tiller to be inspected by the principal warden, Edwin James. James is outside in the night with a rifle, admiring the difficult 500-yard shot that the new inmate previously accomplished when he can barely hit a can at 20. James wonders how the criminal chooses his random targets from such a distance, and get the response "A feeling."

Since his incarceration, Cobb has sought out final imprisonment at Alcatraz, desiring a private cell. James sends him on to his cell but asks for a final shooting pointer, and Cobb advises him to drop his shoulder. James does and hits his target perfectly.

In the present day, Cobb carefully arranges a solitary picnic in a secluded, wooded area high on a San Francisco hill. After he eats his meal, he views two separate couples attending a carnival in the city through a telescope.

Meanwhile, at the comic book store, Doc can't resist hinting at his new consulting position with Hauser's federal task force to one his employees. The employee sounds a "hot chick" alert, and Doc sees that Rebecca has entered the store. She's read Doc's book and wants to talk about the section on her grandfather Tommy Madsen, inmate #2002. While most of the other inmates have several biographical paragraphs in the book, Tommy only received one - it was all the information Doc could find. As Rebecca reveals that she was chasing her own grandfather when her police partner was killed, Doc wonders which inmate will resurface next.

Cobb casually assembles a silenced rifle and calmly shoots and kills one of the couples, then the male partner in the second couple. Later, Rebecca and Doc meet Hauser and Lucy at the crime scene, where Doc recognizes the nearby bodies of dead crows as a trademark of a sniper named Cobb, who meticulously shot his victims through their left ventricle, always staging three shootings in three days before going underground.

When Doc feels uneasy at the murder site, Rebecca sends him on a short walk to compose himself. Lucy reveals that Cobb's shootings always appeared to be random. Rebecca asks Doc what kind of rifle Cobb used in the past. The answer prompts her to realize that Cobb most likely used an older model weapon, something he'd be more familiar with than a current firearm with greater range. That means that the police are looking for a sniper's nest in buildings too far away. Rebecca zeroes in on the actual location on the forested hill nearby, finding an abandoned shell casing to prove it. The hill also provides a clear view of Alcatraz.

In 1960, Ernest Cobb is put off by the presence of fellow inmates during mealtime. Back in his cell, Cobb desperately tries to block out the relentless chatter of the inmate in the cell next to him. Just before he snaps, his attention is diverted by Jack Sylvane throwing a chair and being taken to solitary by the guards after his wife requested a divorce. Cobb is taken by the idea of solitary confinement.

In the secret prison facility for the Alcatraz inmates, Lucy questions the first captured returnee, Sylvane. She asks him if he's working with Cobb and where he's been for the past 50 years. Sylvane notices the security camera trained on him and wants to know who's watching him.

In another room, Hauser observes on a video monitor as Sylvane explains that he doesn't know how or why he woke up in the present day. Lucy asks about the key found on him, which he'd retrieved from the mysterious Barclay Flynn. Sylvane insists that he doesn't know anything about it, and the advanced lie detector technology Sylvane's hooked in to reveals that he's telling the truth.

In the hidden room in the Alcatraz guard barracks, Rebecca retrieves Cobb's files as Doc talks in the dark about the scope and secrecy of Hauser's operation. She reminds him that they were the ones who captured Sylvane. Encouraged, Doc explains that Cobb spent more time in solitary than any other prisoner at Alcatraz.

After Hauser and Lucy reveal that the shell casing matches the kind of weapon Cobb preferred, Rebecca and Lucy pay a visit to Whitten, a familiar source on the shadier side of the gun business. Shown a photo of Cobb, he at first denies having encountered him, but when Whitten hears of the crime Cobb committed, he admits that he sold a vintage Winchester to a man who used an untraceable prepaid credit card. Inspecting security footage from Whitten's store, Doc and Rebecca spot Cobb's distinctive hotel room key and start to try to identify it. Meanwhile, Cobb assembles his rifle in a small, dank room, preparing for his next strike.

Flashing back to 1960, Cobb meets with Warden James, who is eating dinner. James recounts how he procured fine knives for Alcatraz against conventional wisdom, but what strikes Cobb most is the realization that the warden prefers to eat alone. James then reads from a politely worded letter Cobb had sent him, requesting to be interred in solitary or on a cellblock where prisoner interaction is prohibited. James praises the letter but denies the request. Cobb practically begs for solitude, but James dismisses him so that he can conclude his meal privately.

As Rebecca investigates at the fleabag hotel, Doc questions Lucy about what she knows about how they inmates are returning. How does she just accept everything that's been happening? Lucy tells him how she feels about it doesn't change the fact that it is happening. They investigate Cobb's rented room, and Lucy opens a curtain to discover a message written on the window pane: "I Can See You," with an image of a target. Before Rebecca can warn her to get down, Lucy is shot through the chest by Cobb.

Hauser arrives at the scene as paramedics load the critically injured Lucy into an ambulance; he orders Rebecca to find Cobb. Rebecca tells him that Cobb played them and demands to know if the Alcatraz inmates know that the task force is after them. Hauser won't reveal any more information and insists that Rebecca use the information she has to stop Cobb.

At the hospital, Rebecca tries to wash Lucy's blood off of her, and she loses her composure in the bathroom. Doc tells Hauser that Lucy survived her surgery but has fallen into a coma that may or may not be temporary.

Hauser confronts Sylvane in the secret facility; he shows him a photo of Lucy and demands to know if she was a target. Sylvane insists that he doesn't know, and Hauser warns him that perhaps "Dr. Beauregard can jog your memory."

Rebecca and Doc try to identify a pattern hidden within Cobb's seemingly random sniper assaults. They realize that every shooting spree has taken the life of a female victim approximately 16 years old. Rebecca wonders if there's a significant 16-year-old girl in Cobb's history. Doc tells her that Cobb grew up in an orphanage and sought out his birth mother only to be rejected, but his mother's age doesn't line up with that of the victims. What do the girls mean to Cobb?

Doc finds an undelivered letter sent to Cobb in the Alcatraz files. The letter was sent by Eloise, Cobb's 16-year-old half-sister who witnessed their mother's rough rejection of him - she was reaching out in hopes of gaining a big brother who would look out for her.

Cobb never received the letter, and Doc surmises that Cobb saw that his mother had a second child whom he imagined received all the love and attention he did not, and he's acting out his revenge against his "rival" sibling, now deceased herself, in his shootings.

Back in 1960, Cobb refuses to stand in his cell to be counted by the guards and receives a beating ordered by Tiller; his disobedience lands him his much-desired stint in solitary.

In the present day, sitting in Cobb's cell, Rebecca creates a makeshift telescope from a magazine and eyeglasses. Rebecca realizes that Cobb must have done the same thing from his Alcatraz cell. Seeing all the people of San Francisco as such easy, plentiful victims is what's kept him in the city so far.

Meanwhile, Cobb sets up another picnic on a high vantage point atop a building and launches into a new, large-scale killing spree on a densely populated shopping center.

Back in 1960, Warden James visits Cobb to praise him for his cleverness in choosing the smallest possible infraction that would result in solitary confinement. But James does not like being manipulated, and to reassert his power he installs Cobb's ceaselessly talking, probably schizophrenic cellblock neighbor in his solitary cage with him, sending Cobb into howls of protest.

After learning of the shopping center shootings, Rebecca believes that Cobb broke from his pattern: Lucy was not his formal second shooting, and they still have one more chance at capturing him. Using computer models, they narrow their search down to the tallest buildings Cobb could have viewed from his cell in 1963, settling on two prime neighboring structures that each offer a promising vantage point over crowd-gathering attractions.

As Rebecca and Hauser split up to investigate, Rebecca discovers Cobb in position and ready to start shooting. They exchange fire, and as Hauser quietly positions himself to back her up, Rebecca risks setting her gun aside to get Cobb to listen as she reveals the truth about his half-sister. The distraction works long enough for Rebecca and Hauser to tackle Cobb and take him down. Hauser then shocks Rebecca by shooting Cobb through his right hand to prevent him from ever firing a rifle again.

As Lucy lingers on life support, Doc confesses to Rebecca that he doesn't know if he's cut out for the task force. He realizes that he's not in the comic book world anymore and that real people will die if they don't stop the Alcatraz inmates. She assures him that it's all part of the job, and though he fears he won't be good it, she thinks he already is.

Hauser installs Cobb in his secret prison, warning him that he could have killed him - and that Cobb may soon wish he had. Cobb then flashes back to the 1960s: he's straight-jacketed after having seemingly gone insane after James' punishment, but James hopes to bring him back by introducing him to someone important. Lucy appears, introducing herself as Lucille Sengupta and telling him, "I'm here to help you."