Marine General Francis Xavier Hummel(Ed Harris) has spent most of his career carrying out covert operations, but there's no record of these operations. Over the years, nearly a hundred of his men have been killed but have not received any recognition. After trying to get them that through normal channels, Hummel now decides that it's time for drastic measures. He and some other marines take some rockets that are equipped with a biological weapon. They then go on a tour of Alcatraz, and take the tourists hostage. He then calls the Pentagon and informs them that unless they pay him 100 million dollars as reparation for him, he will launch the rockets. Now the Pentagon doesn't want to capitulate. So they decide to send in a team of Navy Seals. Now they need someone who knows Alcatraz and the best person they could find is John Patrick Mason(Sean Connery), a man who escaped from Alcatraz, and who has been in prison in the U.S. for the past 30 years. Also accompanying them is Stanley Goodspeed(Nicolas Cage), an FBI chemical weapons expert. When they go in, the Marines ambush the Seals. Only Mason and Goodspeed are left, and the two have to try and neutralize the weapons. Only problem is, that Goodspeed is not really a man of action and Mason knows that when he returns, he will be sent back to prison, and Mason doesn't really deserve that.