In the present day, a man 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. He casually assembles a silenced rifle and calmly shoots and kills one of the couples, then the male partner in the second couple.
Flashing back to 1960, the same man, Ernest Cobb, is brought into Alcatraz for the first time. He is 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, attempting the replicate the difficult long-distance shot the new inmate previously accomplished. James wonders how the criminal chooses his random targets from such a distance. Cobb's response: "A feeling."
Since his first incarceration, Cobb has sought out final imprisonment at Alcatraz, desiring a private cell. James sends him on to his cell, but he asks for a final shooting pointer. Cobb advises him to drop his shoulder. James does and hits his target perfectly.
At the comic book store in the present day, Doc can't resist hinting at his new consulting position with Hauser's federal task force to one his employees. Meanwhile, at the police station, Rebecca's fellow officers tease her about taking a federal assignment. But her fiancÃ�ï¿½Ã�Â©, Jimmy, more seriously questions her decision, especially because she didn't consult him before making her choice. Nevertheless, he says that he accepts her decision.
Lucy drives Hauser to a senior care facility, where he meets with - and smuggles a bottle of booze to - his elderly colleague Paul, the prison guard who discovered the empty Alcatraz alongside Hauser in 1963. Hauser tells him that the inmates have begun to resurface, and that he captured the first one back: Jack Sylvane. Hauser also informs Paul that E.B. Tiller was killed by Sylvane, and he and Paul agree that Tiller was a good man. But Paul's advancing senility causes him to circle back in conversation, and Hauser ends the visit - but not before Paul urges him to find the prisoners because he is "the only one left."
In 1960, Ernest Cobb is put off by the presence of fellow inmates during meal time, eager for solitude. In his cell, he desperately tries to block out the relentless chatter of the inmate in the cell next to his. Just before he snaps, his attention's diverted by Jack Sylvane throwing a chair and being taken to solitary by the guards after his wife requests a divorce.
Back in the present day, Cobb watches the crime scene from his secluded perch, studying Hauser and Lucy through his telescope. Doc recognizes that the prisoner number Hauser mentions was most recently on the Alcatraz uniform belonging to Ernest Cobb, a sniper who always meticulously shot his victim through their left ventricle.
When Lucy suggests that Doc take a short walk for relief from what he's viewed at the crime scene, he finds the bodies of dead crows - something he recognizes as a trademark of Cobb's. Hauser sends Rebecca and Doc to question a homeless man who was found wearing Cobb's abandoned uniform, and he asks Lucy to keep an eye on them.
Still unsure that all inmates will resurface still looking as young as when they disappeared - as Sylvane did - Rebecca shows the homeless man photos of both the youthful and a CG-aged Cobb. The homeless man recognizes them as the same person, and he reveals that the younger version shared a flophouse with him. Investigating the flophouse, Lucy opens a curtain in Cobb's rented room to discover a message written on the window pane: "I Can See You" with a target. Before Rebecca can warn her to get down, Lucy is shot through the chest. Hauser arrives at the scene as paramedics load the critically injured Lucy into an ambulance, and he orders Rebecca to find Cobb.
Flashing back to 1960, Cobb meets with Warden James at a one-sided diner in which 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 sent him, making requests to be interred in solitary or on a cell block where prisoner interaction is prohibited. James praises the letter but denies the requests. Cobb practically begs for solitude, but James dismisses him so that he can conclude his meal privately.
Shaken by Lucy's shooting, Rebecca and Doc try to identify any pattern to Cobb's seemingly random sniper assaults. They realize that every shooting spree has taken the life of a female victim approximately 16 years old, and Rebecca wonders if there's a significant girl of that age 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 properly.
Suspecting that Cobb is brazen enough to taunt them, Doc realizes that Cobb's flophouse alias, "Eddie Jones" is a clue: the intersection of Eddy and Jones Streets, where a busy superstore offers an expansive parking lot ripe for a sniper attack. Arriving at the scene, shoppers quickly begin dropping from sniper fire, and Rebecca and Doc are in the midst of a full-blown attack.
Hauser confronts Jack Sylvane in the secret facility where he's been imprisoned, holding a photo of Lucy. Sylvane insists that he doesn't know who she is, even after Hauser gives him a beating. Sylvane does admit that he remembers Hauser somehow, but he doesn't know from where or how, and he insists that he doesn't know who took him from Alcatraz. Hauser suggests that Dr. Beauregard may jog Sylvane's memory.
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 the hope of gaining a big brother who could 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. Cobb is acting out his revenge against his "rival" sibling, now deceased herself, in his shootings.
Creating a makeshift telescope from a magazine and eyeglasses, Rebecca realizes that Cobb did the same thing from his Alcatraz cell. She says that seeing all the people of San Francisco as such easy, plentiful victims is what's kept him in the city so far.
Back in 1960, Cobb refuses to stand in his cell to be counted by the guards, and he receives a beating. His disobedience lands him his much-desired stint in solitary. Warden James visits him to praise him for his cleverness in choosing the smallest possible infraction that resulted in solitary. But James does not like being manipulated, and to reassert his power he installs Cobb's chatty cell block neighbor in his solitary cage with him, sending Cobb into howls of protest.
In the present, Cobb sets up another picnic on a high vantage point atop a building, while Rebecca and Doc try to determine where he'll strike next. 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.
Rebecca and Hauser split up to investigate, and Rebecca discovers Cobb in position and ready to start shooting. As Hauser quietly positions himself to back her up, Rebecca risks setting her gun aside to get Cobb to listen to her 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, but Hauser shocks Rebecca by shooting Cobb through his right hand to prevent him from firing a rifle ever again.
Hauser and Rebecca arrive at the hospital, where Doc informs them that Lucy has survived her surgery but remains a coma. As Hauser checks on Lucy, Rebecca surreptitiously reveals to Doc that Jack Sylvane slipped her an unusual piece of glass that she's kept from Hauser. Doc thinks it might be part of a silver photo plate, the kind used for making images in the late 1800s.
Rebecca heads to her Uncle Ray's bar, where a tipsy Jimmy takes shots lined up by Ray: he's celebrating his promotion to detective. As Jimmy walks home, Rebecca confronts Ray about her grandfather Tommy, who was an Alcatraz inmate - not a guard, as Ray had claimed her whole life. She demands to know what Tommy did to be sentenced to Alcatraz, and Ray reluctantly tells her that Tommy killed her grandmother. The news shakes Rebecca to the core.
Hauser installs Cobb into his secret prison, warning him that he could have killed him and Cobb may soon wish he had. Cobb flashes back to the 1960s: he's straightjacketed 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."