FBI Special Agent Ellen "E. Z." Williams (Claudia Christian) and her team show up to nail Nick, but things go bad, and Sascha gets shot.
After eight months of recovery following his brief bout of being clinically dead from the shooting, Sascha is incarcerated along with Nick in the newly reopened Alcatraz prison.
Run by the charismatic warden, Juan Ruiz "El Fuego" Escarzaga (Tony Plana), the place is known for its new state of the art death chamber where the condemned can choose from five different ways to die -- lethal injection, gas chamber, hanging, firing squad, or electric chair.
Lester McKenna (Bruce Weitz) is the first prisoner scheduled to be executed. An older man, he stole $200,000,000 worth of gold bricks in a heist that resulted in five deaths.
Federal Bureau of Prisons head Frank Hubbard (Stephen J. Cannell) and Supreme Court Justice June McPherson (Linda Thorson) have arrived to witness the execution, which is a result of June sentencing Lester.
But she's not the only one interested in Lester. A small but well-equipped team of terrorists who call themselves the "49ers" have parachuted onto the island, and gained control of it.
When Lester won't tell them, Donny shoots a nearby priest (Eva-Maria Schönecker), and threatens to kill others if the info isn't delivered.
Donny's plan is disrupted, however, when Sascha decides to step in and fight back. It turns out that Sascha is actually an undercover FBI agent who's been trying to use Nick to get to Sonny Eckvall.
When Sascha rescues Lester, the 49ers strap June to the electric chair and threaten to kill her, all while Ellen and her team prepare a rescue plan from the mainland.
With the help of Nick and some of the other inmates such as Twitch (Ricardo "Kurupt" Brown) and Little Joe (Michael "Bear" Taliferro), Sascha sets out to rescue June and bring Donny down, before Alcatraz becomes everyone's final resting place.