Rogue Force Recon Marines, under the command of the valiant Brigadier General Francis Hummel, take control of a cache of rockets armed with VX gas, an exceptionally toxic chemical weapon, from a Naval Weapons Depot. Alongside his second-in-command Major Tom Baxter (David Morse), Hummel seizes Alcatraz Island, taking 81 tourists hostage and locking them in prison cells. He threatens both the FBI and the Pentagon with the launch of the VX rockets against San Francisco unless the government provides a ransom of $100 million from a military slush fund. This money is intended to support his men and the families of Recon Marines who perished on covert missions he commanded, but for whom no compensation was offered.
In response, the Pentagon and FBI concoct a plan to regain control of the island using an elite Navy SEAL team led by Commander Anderson (Michael Biehn). To assist in neutralizing the VX threat, they enlist chemical weapons specialist Stanley Goodspeed, who, despite not being a field agent, finds himself the only expert available for the critical task.
To gain vital information about Alcatraz's layout, FBI Director Womack (John Spencer) releases federal inmate John Mason, the sole person to have escaped from Alcatraz successfully. Mason, lured in by the promise of a pardon, quickly realizes Womack has no intention of honoring that deal. After making a brief escape to reconnect with his estranged daughter Jade Angelou (Claire Forlani), Mason is soon tracked down by Goodspeed and the FBI.
Upon entering Alcatraz, Mason and Goodspeed encounter unexpected obstacles—the prison is equipped with sensors installed by Hummel’s team, alerting them to their presence. In a tense confrontation, only Mason and Goodspeed manage to escape. Eager to fulfill their mission, Goodspeed pressures Mason for assistance, but the latter seizes the moment to escape from custody, before reconsidering his stance for the sake of his daughter’s safety.
Together, they take down several squads of Marines and manage to disable twelve out of fifteen rockets by extracting their guidance chips. Meanwhile, the FBI readies strike fighters armed with plasma to obliterate the island alongside the gas. Mason reveals to Goodspeed that, as a British agent, he stole microfilm containing sensitive secrets about U.S. and global leaders, sourced from the files of former FBI Director J. Edgar Hoover. After resisting for 33 years, he was imprisoned for refusing to disclose its location.
Hummel escalates the situation by threatening to kill a hostage unless they surrender the stolen chips; Mason heroically destroys them before attempting to negotiate with Hummel, buying time for Goodspeed. Although Goodspeed manages to disable another rocket, he is captured in the process. However, Mason comes to the rescue just as the deadline approaches. Hummel initiates the launch, only to destroy the warhead at the last moment.
When he faces Captains Darrow (Tony Todd) and Frye (Gregory Sporleder), Hummel clarifies that the entire rocket threat was a mere bluff; he never intended to harm innocents. He concludes the mission and instructs his Marines to leave Alcatraz with a few hostages and one remaining rocket as cover for their retreat, while accepting full responsibility. However, his men revolt, demanding payment for their efforts. A fierce gunfight ensues; Baxter sacrifices himself for Hummel, who is fatally injured. In his dying moments, the general reveals the location of the last rocket to Goodspeed.
As Goodspeed retrieves the VX globule, he is attacked by one of Hummel's men, resulting in a struggle during which Goodspeed smashes the globule into the attacker's mouth, killing him instantly. He then injects himself with a vaccine to guard against imminent death. Though Goodspeed signals that the danger has passed, an accidental bomb drop from a jet sends him flying into the bay, where Mason saves him.
In the aftermath, Goodspeed falsely reports that Mason was killed during the event. The film concludes with Goodspeed sprinting from a church in Ft. Walton, Kansas, as his pregnant wife Carla urges him to hurry and escape with her. Holding a canister containing the microfilm Mason directed him to, Goodspeed glances at its contents and asks Carla if she would care to learn the true story behind JFK’s assassination.
