A group of rogue U.S. Force Recon Marines, led by disenchanted Brigadier General Frank Hummel (Ed Harris) and his adjutant Major Tom Baxter (David Morse), seize a stockpile of deadly VX gasâarmed M55 rockets; Hummel loses one of his own men in the process when one of the VX canisters ruptures. The next day, Hummel and his men seize control of Alcatraz Island and take eighty one tourists hostage. Hummel threatens to launch the rockets against San Francisco unless the government pays $100 million from a military slush fund, which he will distribute to his men and the families of Recon Marines who died on clandestine missions under his command and whose deaths were not compensated.
The Pentagon and FBI develop a plan to retake the island with a U.S. Navy SEAL team led by Commander Anderson (Michael Biehn), enlisting the FBI's top chemical weapons specialist, Dr. Stanley Goodspeed (Nicolas Cage). Goodspeed's confidence, already shaky as he is a "lab rat" with minimal combat training and experience, is further tested when his fiancÃ©e Carla (Vanessa Marcil) reveals she is pregnant.
FBI director James Womack (John Spencer) is forced to turn to federal prisoner John Mason (Sean Connery), a 60-year-old British national who has been imprisoned without charges for three decades. Mason is the only Alcatraz inmate ever to escape the island, doing so in 1963 through uncharted underground tunnels.
While in custody at the Fairmont Hotel, Mason flees. He steals a Hummer H1 and Goodspeed pursues in a commandeered Ferrari F355, resulting in a chase through the streets. Mason seeks out his estranged daughter Jade (Claire Forlani); Goodspeed arrives with a team to re-arrest Mason, revealing to Jade that he is aiding the FBI.
Goodspeed, Mason, and the SEALs infiltrate Alcatraz. However, Hummel's rogue Marines are alerted to their presence and ambush them in a shower room. All the SEALs, including Anderson, are killed, leaving only Mason and Goodspeed alive. Mason sees his chance to escape custody and disarms Goodspeed, but Goodspeed convinces him to help defuse the rockets, since Mason's daughter is also at risk.
Mason and Goodspeed eliminate several teams of Marines and disable 12 of the 15 rockets by removing their guidance chips. Hummel threatens to execute a hostage if they do not surrender and return the guidance chips. Mason destroys the chips, then surrenders to Hummel, trying to reason with him as well as buy Goodspeed some time. Though Goodspeed disables another rocket, the rogue Marines capture him. With the incursion team lost, the military initiates their backup plan: an airstrike by F/A-18s with thermite plasma, which will neutralize the poison gas but kill everyone on the island.
Mason and Goodspeed escape, and Mason explains why he was held prisoner: he was a British SAS Captain who stole a microfilm containing details of the United States' most closely guarded secrets, refusing to give it up when captured because he knew he would be killed if he did. When the deadline for the transfer of the ransom arrives, Hummel and his men fire one of the operational rockets. During the launch of the rocket, Hummel changes the coordinates and diverts the rocket away from its original target and instead detonates at sea. Hummel then reveals that the mission is over and it was all a very elaborate bluff, as he never had any intention of taking innocent lives. When confronted by two of his men, Captains Frye (Gregory Sporleder) and Darrow (Tony Todd), Hummel orders them to exit Alcatraz with a few hostages and the remaining rocket to cover their retreat, while he will assume blame. Realizing they will not be paid their $1 million apiece, Frye and Darrow mutiny against Hummel and Baxter, killing the latter and mortally wounding the former.
Darrow and Frye proceed with the plan to fire on San Francisco. While Mason deals with the remaining Marines, Goodspeed seeks out the last rocket, which Hummel reveals the location of with his dying breath. As the jets approach, Goodspeed kills both Darrow and Frye, disarming the rocket. He signals the jets that the threat is over but not before one jet releases a bomb on the island. Though no hostages are injured, Goodspeed is thrown into the sea by the blast before Mason rescues him.
Goodspeed tells Mason that Womack tore up his pardon, then informs his superiors that Mason was killed in the bomb explosion. Mason gives Goodspeed a note that holds the location of the microfilm and the two part ways. Some time later, Goodspeed and Carla recover the microfilm containing a half-century of state secrets, including who actually killed John F. Kennedy.
What do Hummel and his men seize control of?
Alcatraz