On a rainy morning at Arlington National Cemetery, Brigadier General Francis Hummel (Ed Harris
) visits the grave of his wife, Barbara, who had recently passed away from an illness. He tells her that he misses her, but there is something he has to do now, and most of the world isn't going to like it. He hopes that wherever she is, she understands that he did what he had to do. After saying a final goodbye, he places his Medal of Honor on the headstone before he leaves.
Later that night, Hummel leads a group of rogue Force Recon Marines on a raid of a Naval Weapons Depot. They seize a stockpile of rockets armed with weapons grade O-ethyl methylphosphonothioic acid, more commonly known as VX gas. They lose one of their men in the process, a horrific death caused by an accidental release of the chemical when one of the canisters was dropped and a sphere containing the deadly substance shatters.
In an FBI lab in Washington DC, Dr. Stanley Goodspeed (Nicolas Cage
) is called in to inspect a package sent to Bosnian refugees. He and a trainee, Marv Isherwood (Todd Louiso
), find a small doll inside that sprays them with sarin gas and contains a bomb made of C4 explosive that could destroy the lab and kill everyone in the building. As Stanley works frantically to disarm the bomb he turns down a hypodermic needle loaded with a dose of atropine. Stanley disarms the bomb successfully. At home that night, he relaxes until his girlfriend, Carla (Vanessa Marcil
) arrives home. She tells him she's pregnant, and Stanley accepts her marriage proposal.
Hummel is joined by other Marines who have served him over the course of his career; Major Tom Baxter (David Morse
), who he served with in Vietnam, Captain Hendrix (John C. McGinley
), who he served with in the Gulf, and Captains Frye (Gregory Sporleder
) and Darrow (Tony Todd
), who organized the raid on the weapons depot. They seize Alcatraz Island and take 81 tourists hostage, placing them in the prison cells, then threatening the FBI and Pentagon with launching the VX rockets against the population of San Francisco, unless the government pays ransom and reparations to the families of Marines who died on illegal, clandestine Marine Force Recon missions ("Black Ops") that were commanded by General Hummel.
After Goodspeed makes love to Carla, he receives a call telling him to report to San Francisco. He assures her that it is probably just a training exercise, and they can be married there when it is finished. When he arrives, he is greeted by senior agent Ernest Paxton (William Forsythe
) and Bureau Director James Womack (John Spencer
). They brief him on the situation, asking him to consult. Goodspeed agrees, but asks Paxton for a gun having left his own sidearm at home. SEAL Commander Anderson (Michael Biehn
) offers to lead an incursion team to the island to neutralize the warheads and free the hostages. In need of reliable first-hand knowledge of the physical layout of Alcatraz, Womack is forced to turn to long-time federal prisoner John Mason (Sean Connery
), the only former inmate of Alcatraz to ever successfully escape. There is a considerable amount of bad blood between Mason and Womack, so Goodspeed is tasked with talking to him. Mason is willing to cooperate, however, shortly after he signs his pardon, Womack tears it up. Goodspeed notes that while they were talking to Mason he mentioned the names of several historical figures who were wrongfully imprisoned like Nelson Mandela, Sir Walter Raleigh, Archimedes and Aleksandr Solzhenitsyn. Womack brushes it off, accusing Goodspeed of asking too many questions.
Part of Mason's agreement includes a short stay at a luxury suite at San Francisco's Fairmont Hotel. He calls in a large amount of food to distract his minders. Out on the suite's balcony, Mason, while shaking on the deal he made with Womack, slips a rope around Womack's wrist and throws him over the side, holding the rope. When Goodspeed calls the other agents to help him pull Womack to safety, Mason escapes. He steals a Humvee from a hotel patron and drives recklessly through San Francisco, colliding with cars and other obstacles to block the pursuit of him. He finally makes it to the Palace of Fine Arts and meets with his daughter, Jade (Claire Forlani
). The two seem to reconcile, Jade being bitter after her mother's death and Mason's (unintentional) abandonment. Goodspeed shows up and tells Mason they have to rejoin the FBI team. Upon their return, Goodspeed learns that he himself will accompany Mason and the incursion team to Alcatraz, despite his minimal combat training and fear of deep water. Paxton appeases him by having his men get Carla to safety.
With Mason's guidance, the SEAL incursion team successfully infiltrates Alcatraz undetected, but as they work their way through the tunnels of Alcatraz and enter the shower room, their presence is detected by sophisticated equipment set up by Hummel's men. Hummel attempts to talk Anderson down, but Frye and Darrow grow impatient and open fire, leaving only Mason and Goodspeed alive. With Mason deciding to leave the island, Goodspeed must reveal the true purpose of the mission. Realizing his daughter's life is at risk, Mason agrees to stay and help.
They begin the process of seeking out and disabling the 15 rockets one-by-one, traveling through the underground catacombs to avoid detection. After twelve rockets are sabotaged by Goodspeed and Mason, Captain Hendrix is ordered to take a fireteam down to the catacombs, resulting in a pitched battle in which Goodspeed uses lethal force for the first time. After learning that Hendrix's squad has been killed, Hummel threatens to execute one of the hostages unless the guidance chips of the sabotaged rockets are returned to him. Goodspeed grapples with the idea of surrendering the chips for a few moments until Mason destroys the chips, then surrenders to Hummel to buy time for Goodspeed to disable more rockets. During a tense confrontation in the prison courtyard, Mason insinuates that Hummel is actually insulting the memory of his fallen soldiers by threatening innocent civilians, and tests the general's resolve by calling him an idiot and denouncing his sense of patriotism as "a virtue of the vicious." (he quotes Oscar Wilde). Hummel angrily strikes Mason and prepares to shoot him in the head, but instead orders him locked up. Goodspeed is able to disable the thirteenth rocket just before he is captured. Meanwhile, realizing that the SEAL team is lost, the Pentagon readies a backup plan, an attack by armed F-18s that will neutralize the poison gas by releasing thermite plasma bombs, which would also kill everyone on the island.
Paxton confronts Womack, asserting that given the severity of the situation, he has earned the right to know why Mason was imprisoned, and why Womack hates him so much. Womack reveals that Mason was a Captain for the British SAS. He stole a microfilm containing serious secrets about U.S. and other world leaders and events. The information came from the personal files of former FBI Director J. Edgar Hoover. Mason was captured at the Canadian border and refused to divulge the location of the microfilm. After being disavowed by the SAS, he was kept locked up, without benefit of trial, and told he would not be released until he gave up the microfilm. After Hoover died, the agency became a different beast, but it also became harder to come clean about the incident, so Mason remained locked away and forgotten.
Mason is imparting this same information to Goodspeed as he fashions the bedding of his cell into a knotted rope. He explains that the government had no intention of ever letting him go; had he given up the microfilm, they would have simply killed him. Goodspeed furiously asks how he managed to get out of the cell in the first place. An annoyed Mason ignores the question, simply throwing the rope until it finally hits a security switch that unlocks their cell doors. Once they have safely made it to the beach, Mason again decides to leave the island, convinced that Hummel is only bluffing. Goodspeed insists that the military will need more than Mason's assumption to call off the airstrike, and he will finish the mission alone if he has to. Goodspeed is captured before he can find another rocket, but he's rescued by Mason, who decided to come back, he did not want to see Stanley's child grow up without a father, as Jade has.
The deadline Hummel gave the FBI/Pentagon arrives, and when there is no ransom paid and more time requested, Major Baxter demands he take action. Hummel orders a rocket fired. It's headed for a full stadium at Candlestick Park, but Hummel secretly enters revised coordinates on his computer keyboard and redirects the rocket so that it falls into the ocean. The surviving officers are furious, as Washington will now believe they are weak and hit them with everything they've got. Hummel tells them that the whole operation was a bluff that the government didn't fall for, and since he's a professional soldier, not a murderer, it's all over. He tells his men to take some hostages and leave, he will surrender and take the heat for it all. Frye and Darrow refuse. They consider themselves mercenaries working for pay, and they want their money, or to make good on the threats. A Mexican standoff ensues, and Mason and Goodspeed arrive just in time to witness its conclusion. As shots are fired, General Hummel and Major Baxter are fatally wounded. As Mason opens fire on the mutineers, forcing them to disperse, a dying Hummel tells Goodspeed that the last rocket is in the lower lighthouse.
Goodspeed heads to the lighthouse while Mason covers him from the rooftops. As Goodspeed disarms the last rocket, Darrow corners him, menacing him with a combat knife. Goodspeed launches the now unarmed rocket, which hits Darrow squarely in chest, causing him to plummet to his death. As Goodspeed is handling the final string of green VX spheres, one of them drops on the deck. He catches it before it can shatter, but before he can safely stash it away, Frye attacks him. With the thermite plasma-armed jets approaching, Frye overpowers Goodspeed and proceeds to strangle him, threatening to choke his million bucks out of him. Out of options, Goodspeed shoves the loose sphere into the captain's mouth and hits him in the jaw, crushing the vial and releasing the contents. Captain Frye dies almost instantly, violently convulsing as his flesh melts away. The liquid also gets on Goodspeed and he immediately stumbles away and pulls the atropine antidote from his boot and injects himself in the heart with it. He is then able to grab and light off two green flares, the prearranged signal that the threat is over. The flares are spotted from land, but only after one of the jet pilots has released his bombs, exploding on the rear of the island, missing all the hostages and sending Goodspeed flying into the sea.
Mason reappears to pull the unconscious Goodspeed to shore. Paxton calls on the radio and learns from Goodspeed that all the hostages are still alive, but that Mason had been killed. That provides Mason time to escape before the FBI arrives. Goodspeed tells Paxton and Womack that Mason was "vaporized" by the thermite plasma missile.
The film ends with Goodspeed running from a church in Ft. Walton, Kansas, as Carla urges him to hurry and get in the car so they can get away. Goodspeed has in his hand a canister containing microfilm. Mason had told him where to find it. He looks at the microfilm and asks Carla if she'd like to know who really shot JFK.