A San Francisco detective takes on a homicide case that leads her to a man who vanished from Alcatraz prison nearly 50 years earlier, and a secret organization that is hunting for hundreds like him.

Detective Madsen and Dr. Soto track a sniper who is targeting young people, and who just wants to be left alone. Soto questions his involvement with the task force after one of the team becomes a victim.

The team launches a manhunt after a child killer from Alcatraz kidnaps a young boy. In the 1960s, the warden tries to get Kit Nelson to confess to the murder of his brother.

A con man from Alcatraz robs a bank but takes only the contents of the safety deposit boxes, but varies from his old M.O. when he visits the owners of the stolen property apparently in search of something.

The team tracks the first Alcatraz guard to resurface in the present day, only to learn that he has a personal connection to Ray and a prisoner he knew inside the Rock.

Rebecca and Diego pursue a military munitions expert who is terrorizing San Francisco with a series of bombs, who was interrogated by Lucy during his time on Alcatraz.

The team tracks a chemistry expert and mass murderer who targets bullies.

The team suspects that a former inmate is repeating his past crime, murdering a girl and leaving her body on a golf course. But Clarence Montgomery may, in fact, be innocent.

A pair of criminal brothers return to modern-day Alcatraz on a stormy night in search of a treasure they believe is hidden in the tunnels beneath the prison, taking Dr. Soto hostage after he discovers them.

When an inmate who once kidnapped a young girl for ransom reemerges in the present day, he kidnaps the grown woman's husband as part of a revenge plot. Meanwhile, Hauser and Rebecca become convinced that her uncle has seen Tommy Madsen.

A brilliant young musician who once murdered his mother tries to work out his angst by recreating the crime in the present day, while in the past Dr. Sengupta attempts to treat him.

An inmate with a history of armored truck robberies returns with an unclear agenda. Lucy awakens from her coma, and Hauser searches the tunnels below Alcatraz for answers to the Rock's secrets.

After a former inmate who holds something Hauser wants checks himself into a psychiatric hospital, Tommy Madsen puts his plan into action with a home invasion. In 1960, Tommy is subjected to a secret experiment that may give him what he wants most.