On the series premiere of Alcatraz…

On March 23, 1963 Alcatraz closed because all the prisoners vanished. They said that all the prisoners were transferred.

Past:
Jack Sylvane has a beef with the deputy warden at the prison, E.B. Tiller.

The doctors are taking vials of blood from the inmates. Another inmate says to Jack that something bad is going to happen.

Jack's wife Sonya wants to leave him.

Present:
Jack Sylvane wakes up inside his cell on Alcatraz.

Meanwhile, Detective Rebecca Madsen, who lost her partner, takes up a homicide case of E.B. Tiller. She discovers fingerprints of Jack Sylvane at the crime scene. The FBI's Emerson Hauser takes over the case.

Rebecca meets up with Dr. Diego Soto who has written a book all about Alcatraz and its inmates. Diego finds Jack's death certificate. Her uncle, Ray Archer, who used to work at Alcatraz, tries to convince her to stay away from the case.

Rebecca heads to Alcatraz with Diego and runs into Emerson and Dr. Lucy Banerjee. They are a part of a special task force.

Jack Sylvane is looking for Barkley Flynn who has a black bag holding a key. He kills Barkley.

Jack goes to find his brother who married his wife, Sonya.

Rebecca stops Jack and learns that someone told him to retrieve the key.

Rebecca discovers her grandfather wasn't a guard but rather an inmate at Alcatraz. He was the man running from her when her partner died.

After Emerson explains that he was there when they all vanished, he offers her a job and Diego Soto becomes her new partner.

Emerson takes Jack into the forrest into a bunker that is an updated prison for the Alcatraz prisoners he catches.