An upturned car smolders in the street as Rebecca clutches her side and writhes in pain on the pavement.
Thirty-six hours earlier, Rebecca shares a drink at Ray's bar with her old captain from the homicide division. She tells him that she believes there was a personal reason her grandfather Tommy Madsen killed her partner, Detective Will Peters, during their rooftop pursuit.
The captain reveals that Peters at the time of his death was under investigation by Internal Affairs for receiving suspicious payments from Broadway Mutual - the company owned by reclusive billionaire and former Alcatraz inmate Harlan Simmons. Even though the investigation was dropped when Peters was killed, the captain advises Rebecca to tread carefully.
A panicked man pounds on the glass wall of a secured psychiatric hospital, pressing a Broadway Mutual business card reading "Joe Limerick" against it until he's allowed entry. Limerick tells the receptionist that he doesn't need a doctor. He says that he was an Alcatraz inmate in 1963 and is seeking a safe, quiet place to hide from the bad people who are pursuing him. His story and demeanor are enough to get him admitted out of concern for his mental health. As he lies back in his new hospital bed, he studies a key in his hand. Limerick is "Ghost," the same man who killed Garrett Stillman to take possession of the key.
In 1960, Limerick shivers in his cell. Neighboring inmate Tommy Madsen wants to know if it's true that Limerick escaped. Limerick confirms it, but he says that the brutal tide kept depositing him back on the island as he attempted to swim to freedom. Madsen explains that Limerick is being held in seclusion because the rest of prison population has been told he died during the escape attempt. Warden James even had a death certificate for him created.
"I guess that makes you a ghost," Tommy tells him. As Tommy is dragged from his cell by guards, the warden confirms his story to Limerick.
Strapped to an examining table in the infirmary, Tommy asks the warden if they'll be taking more of his blood. Warden James informs him that this time they'll be "giving back." Tommy is told by a mysterious, suited man wearing glasses that he's receiving a blood transfusion. As Tommy is suddenly wracked with pain and tastes metal in his mouth, he asks if he's going to die. "Maybe," the man replies.
In the present, Tommy sneaks into a house in the night. Catching the owner unaware, Tommy pistol-whips him, demanding to know where the man's wife is and when she's coming home. As the man insists that he doesn't know, a small girl peers in from the hallway, but when Tommy glances over his shoulder in her direction, she's no longer there. Tommy tells the man that he's going to summon his wife home, while the little girl is visible through the window, running for help.
In the underground prison complex, Dr. Beauregard runs tests on Lucy as she wonders whether Webb Porter's blood will give her the ability to play the violin and, more importantly, why do some of the inmates have the colloidal silver in their bloodstream while others do not? Beauregard says he thought because Lucy was the warden's "prize poodle" that she would know the answer.
Later, Lucy chafes against Hauser's attempts to limit her public exposure based on Ernest Cobb's suggestion that she's a target. She says that he'd just as soon keep her in one of the cells. Just then, Hauser is alerted that Tommy Madsen may have been sighted.
The task force assembles at a police station where the little girl has been taken for protection after being discovered on a parkway. She described running from a man whom the sketch artist has rendered as a dead ringer for Tommy Madsen. But the girl is scared and can't provide her home address information. Doc draws a cat for the little girl as Rebecca charms her into coloring it. Doc leaves the eyes off the drawing, prompting the girl to point out the "forgotten" detail, and Rebecca is able to prompt the girl to recall more.
In 1960, Tommy awakens in a lavish, comfortably appointed hotel room in Nob Hill with a view of the San Francisco Bay and Alcatraz. Warden James enters with room service, offering Tommy breakfast. Tommy wonders if he's died and gone to either heaven or hell. The warden assures him that he hasn't, although he adds, "In any Faustian tale a devil is often needed, however misunderstood."
Tommy not only survived being infused with colloidal silver, he also feels fantastic. The warden tells him that it's resulted in great potential for Tommy - for things he can do for the warden.
In the present day, as Tommy sits in the living room, Tommy's victim, Michael Bradley, struggles free from his bonds in the bedroom and retrieves a hidden handgun. Michael's wife, Georgia, arrives home and is confronted by Tommy, just as Michael appears in the stairwell and fires the gun. Tommy ducks the bullets and takes Michael's wife hostage.
Rebecca gradually gets Michael's daughter to reveal her address, and the task force convenes at the home to discover Michael bleeding on the stairs. Tommy left with Michael's wife ten minutes earlier. Meanwhile, Tommy forces Georgia to stitch up a gunshot wound to his fast-healing leg while they hide in a public bathroom.
Aboard a parked private jet, Hauser meets with the enigmatic Passaris, who appears to be a military officer who shares some history with Hauser. Hauser asks him for a face-to-face meeting with Harlan Simmons but is denied. Passaris tells Hauser that such a task is "above my pay grade."
When Hauser tells him that it's about the return of Tommy Madsen, Passaris wonders if that means that the warden is back, and Hauser says that's what he's trying to find that out. Passaris replies that not even the President can get Hauser a meeting with Simmons, but he offers to let Lucy join him as he flies to Paraguay on a military mission.
As he prepares Lucy's passport, Hauser tells him that Paraguay is "complicated for me, given the last time," and he needs to accompany her long enough to get her safely settled. Passaris orders Hauser to brief the task force.
Lucy shares the brief background info she's compiled on Georgia with Rebecca and Doc: Georgia works in a psychiatric hospital, but they still have many questions about why Tommy would abduct her. Rebecca tries to reason out a theory: If Tommy was Garrett Stillman's handler, and Stillman's mission was to steal something from Harlan Simmons, then based on the new information she has about her partner Will, there could also be a connection between Georgia and Simmons.
Rebecca doesn't know why the '63s are fighting one another, but Hauser says, "I might." Lucy tells Rebecca that Hauser's remark is the closest thing to an invitation to join him in his forbidden control room - "the Bat Cave," in Doc-speak.
There Hauser reveals the two keys in his possession - one recovered from Cal Sweeney, the other from Jack Sylvane after he took it from Barclay Flynn - which should unlock the otherwise impregnable door in the prison's Civil War dungeons. The keys, Hauser explains, belonged to Warden James, and he suspects that Tommy works for him.
Warren, a member of Hauser's scientific team, reveals that they believe the "jump" was caused by an unusual seismic event. Hauser admits that he's giving Rebecca and Doc the information because he has to leave for a few days to take Lucy to a safe location. Lucy overhears his revelation.
Lucy tells them that she's found a connection between Georgia and Simmons: Simmons owns the hospital where Georgia works. Lucy's found that Georgia's retinal scan has recently been used to access the location. At that moment, Tommy is forcing Georgia to help him get into the psychiatric hospital.
In 1960, Warden James and Tommy dine in an Italian restaurant, Tommy's requested payment in return for carrying out the warden's wishes. The warden encourages Tommy to think bigger, given the scope of the task. Tommy reveals that he met his wife at the restaurant, and James tells him to consider him a genie capable of granting him one immediate, perfect wish. What does Tommy want most in the world?
In the present, Tommy and Georgia enter Limerick's room, and Tommy is enraged not to find his quarry. But Limerick quickly appears at the doorway, and Tommy is relieved to see him, asking for the key. Limerick takes off in a run, and Tommy pursues him, dragging Georgia along.
At the secret facility, Dr. Beauregard tells Lucy that the colloidal silver will permanently remain in her bloodstream. He wonders if she'll actually accompany Hauser to the safe location, and she tells him that because Hauser has waited for her for 50 years she can't deny him now. But she admits that Hauser's not the same man she fell in love with. "Part of him is missing," she says.
In 1960, Tommy and the warden watch Tommy's home in Oakland from across the street. Tommy marvels at how much his young son, Van, has grown in the three years since he last saw him. The warden allows Tommy to speak to Van, but Tommy's too-familiar approach frightens the boy into running inside the house. Tommy walks back to the warden, telling him, "I know what I want from you."
In the present day, Tommy corners Limerick at gunpoint. Limerick insists that he doesn't have the key. He's afraid that Simmons will kill him if he surrenders it, but Tommy promises to protect him. "That's not possible," says Limerick, who throws himself out of a window, falling to his death on the street below.
Rebecca and Hauser arrive to discover the body. After spotting Tommy in the window, Rebecca runs into the building to capture him. She discovers Georgia, who's been left unharmed and tells her that Tommy has escaped to the garage. Tommy steals a black car and roars away. Rebecca commandeers a blue Mustang and races off in pursuit.
In 1960, Tommy's brother, Ray, still working as a prison guard, enters a secured room at Alcatraz expecting to see the warden and is surprised to find Tommy. Tommy tells Ray that he wants him to leave Alcatraz. He hands him a packet of documents that will allow Ray to adopt Van. Ray protests, believing that he's ingratiated himself with the warden enough to receive the kind of help James gave Harlan Simmons.
But Tommy shocks Ray with an admission: he deliberately killed his wife. Ray still refuses to leave, but Tommy tells him that the packet also contains Ray's termination papers. When Tommy tells him that he can't look at his face anymore, Ray has no choice but to leave, telling Tommy that he'll never see his son again.
As Rebecca follows Tommy in a dangerous high-speed chase through the busy, hilly streets of San Francisco, Hauser, Doc, and Lucy reunite Georgia with her daughter. The revelation that the man Tommy was after was Joe Limerick confuses Doc, who believed that Limerick died in his escape attempt.
Hauser searches Limerick's body for the warden's third key but comes up empty. Doc tells him that Alcatraz inmates always figured out ways to hide items from the guards. Doc searches the hem of Limerick's pants and discovers the key, but he refuses to hand it over to Hauser until he finds Rebecca. As Doc walks away, Hauser pulls his weapon on Doc, but Lucy keeps him from following through.
Rebecca and Tommy's car chase intensifies until finally she's able to sideswipe him and send his vehicle careening end over end until it finally crashes to a stop in the street. As a fire begins to spread, Rebecca scrambles to the car and pulls a stunned Tommy out of the wreckage before it explodes.
Rebecca holds her gun on Tommy as he tries to talk her down, telling her that he's her grandfather. "And you think that makes us family?" she asks. "I don't know you." He tells her the reason that he killed her partner: Will Peters was being paid to watch Rebecca to get to Tommy - the whole thing is the result of Harlan Simmons breaking a promise to Warden James.
Still trying to get to Rebecca, Tommy asks her what her parents were like, then wants to know if Ray told her how they really died. The question catches her off-guard, and Tommy's able to spin around and stab her with a hidden blade, lowering her to the ground and taking her gun before escaping in the Mustang. Seconds later, Doc pulls up and runs to Rebecca's side.
Rebecca is rushed into emergency surgery, and as they wait for news of her condition, Hauser tells Lucy that this situation is exactly why he wants her to leave; Lucy counters that it's exactly why she needs to stay. She might be safer in some remote, wireless village, but she won't allow him to try to complete his life's work without her - they will do it together.
Hauser insists that he will not lose her for a third time, but she tells him that if they can survive a half-century time-jump and a bullet to the heart, nothing can come between them.
Ray arrives at the hospital and when he learns that Tommy is responsible, he grows enraged, telling Hauser that he warned him this would happen. He orders Hauser out of the hospital - but not before he recognizes Lucy from Alcatraz. As Hauser leaves, Doc hands over the third key. Hauser tells him he can join them at the vault if he wants, but Doc believes it's more important to stay at the hospital for Rebecca.
Hauser and Lucy arrive at the third vault, where Hauser uses the third key to successfully unlock it. They step inside and turn on the power, finding an unusual control room inside.
On the wall hangs a map of the United Stated, studded with illuminated electronic pinpoints that spark to life at Lucy's touch. As they see pinpoints labeled with inmate numbers clustered around San Francisco but spread across the United States, they realize that the marked locations track the projected arrival points for the '63s and their appearances aren't just limited to the Bay Area. "They're everywhere," Hauser says.
In 1960, Tommy joins Warden James in the vault, where the mysterious man in glasses who'd earlier been in the infirmary marks the initial arrival points of the first time-jumped inmates. All the locations correspond with spots visited by the warden earlier in the day, and the warden admits that his "best intentions" could not be carried out without the benefit of the mystery man's science.
The man tells Tommy that he's had his eye on him since 1952, and Tommy wonders if the man also served in Korea. The warden tells Tommy that this is his future - he's going to be their "advance man," which Tommy takes as the one who's likely the first to die. When the mystery man confirms their agreement, he dangles an intriguing carrot before Tommy: despite his life sentence, in three year's time, Tommy could be a free man.
In the present day, a loud noise in the vault alerts Hauser and Lucy, who investigate and discover the mystery man lying on the floor, disoriented. The man asks what year it is, and when Hauser tells him it's 2012, he begins to laugh uncontrollably.
In the emergency room, the doctors furiously attempt to revive Rebecca with EEG paddles, but their efforts prove fruitless. As her heart rate continues to flatline, they give up and call her time of death.