- Years ago when the most dangerous prisoners of Alcatraz mysteriously disappeared, they resurface in the present day as part of a larger conspiracy, leaving a police detective, an expert on Alcatraz and an FBI agent to track them down.
- Fifty years ago, Alcatraz prison was closed, all inmates officially shifted to a more modern facility. In fact jailer Emerson Hauser was among those who witnessed dozens of hardened criminals disappearing mysteriously at once. He joined the FBI and heads a secret division to hunt them down now. The first target is Jack Sylvane, dubiously convicted and mistreated, who now exacts bloody revenge on long-retired deputy warden E.B. Tiller. The affair allows recruiting Alcatraz-obsessed genius Dr. Diego Soto and San Fancisco PD detective Rebecca Madsen, who seems somehow destined.—KGF Vissers
- Detective Rebecca Madsen and Alcatraz historian Dr Diego Soto team up with a secret agency that is dedicated to finding and catching inmates from the infamous prison who went missing 50 years ago and are reappearing today.—Fox Publicity
- An introductory voice over informs us that Alcatraz prison was closed on March 21st, 1963, officially because of the crumbling state of the facilities. However, this is not what "really" happened.
On March 20th, 1963, an older guard and a younger guard arrive at Alcatraz. When no one meets them at the dock they proceed into the prison where they find all the cells empty and all the guards missing.
In the present day, a girl on a tour of Alcatraz discovers a man sleeping in one of the solitary confinement cells. The man, somewhat surprised by his surroundings, makes his way off of Alcatraz and, consulting a book on the history of the prison, sees a picture of himself, Jack Sylvane.
A flashback shows Sylvane as an inmate in Alcatraz being harassed by Deputy Warden E.B. Tiller. In the present, Sylvane sees a picture of an elderly E.B. Tiller accepting an award.
SFPD Detective Rebecca Madsen and her partner are chasing a suspect across the rooftops of San Francisco when her partner falls to his death. Three months later, Madsen is still mourning his loss and refuses to take another partner. She responds to a homicide call, the victim of which turns out to be retired prison official E.B. Tiller. However, just as her investigation is getting started she is ordered off the case by a mysterious federal official named Emerson Hauser.
Swiping some evidence from the scene, Madsen discovers Jack Sylvane's fingerprints at the scene. Discovering that Sylvane and Tiller were both at Alcatraz, she consults Alcatraz expert Dr Diego Soto. From Soto she learns that Sylvane supposedly died thirty years before.
Madsen and Soto meet with Madsen's "Uncle", Ray Archer. A former guard at Alcatraz, Ray raised Madsen after her parents' deaths and, according to her, had been best friends with her grandfather, Tommy Madsen, another guard.
Madsen and Soto travel to Alcatraz, seeking to find a hidden room of records that Soto had previously stumbled upon. Sneaking into the off limits cellars of Alcatraz they find the records room but are gassed into unconsciousness. They wake up in a high tech command center on Alcatraz and are confronted by Emerson Hauser and his assistant Lucy Banerjee. Hauser and Banerjee show Soto and Madsen surveillance tape showing Jack Sylvane in the present day, unaged.
In 1960, Jack Sylvane is in the Alcatraz infirmary getting blood drawn and talks to a mysterious fellow prisoner hidden behind a sheet. In the present day, Sylvane shoots two cops outside the house of a man named Barclay Finn. He then forces Finn to open his safe and give him the contents: a soft black bag. Sylvane then murders Flynn.
Responding to the crime scene, Madsen is informed by Soto that Jack Sylvane's wife married Jack's brother after he disappeared. Jack goes to confront his brother Allen, who is astonished to see his brother alive and unaged. Jack then goes to his wife's grave, where Madsen finds him. Holding him at gunpoint she questions him about why he killed Barclay Finn. Sylvane responds that he only did what "they" told him to do. When Sylvane begins to raise his gun, he is shot by Emerson Hauser and Madsen arrests him.
Back at Alcatraz, Hauser shows Madsen and Soto a room filled with pictures of the "Sixty Threes", the 256 prisoners and 46 guards who were on Alcatraz on March 20th 1963. Hauser explains that all the Sixty Threes disappeared mysteriously and are now coming back. A flashback to 1963, shows that the younger guard who discovered Alcatraz empty was Emerson Hauser. Looking at the wall of photos, Madsen sees a picture of her grandfather Tommy Madsen and realizes he was an inmate, not a guard. She also recognizes him as the suspect that she and her partner were chasing when he died. Madsen demands to be let in on the investigation into the Sixty Threes and Hauser gives her her transfer orders. They agree to bring Soto on as her partner.
The final scene shows Hauser leading Jack Sylvane to an isolated bunker in the woods. Inside, is a high tech prison with a cell block built to resemble that of Alcatraz. Hauser locks him in a cell and informs him he won't be alone in the prison for long.
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