The Rock

Brigadier General Francis X. Hummel (Harris) is disgusted by the way the government abandoned many of his men after sending them on illegal suicide missions. He assembles a rogue team of 14 elite U.S. Marines (Force Recon), most of whom have previously served under him, though Captains Frye and Darrow are new. Hummel attacks a naval weapons depot, taking fifteen VX missiles. He loses one of his men during the attack, when a ball of VX gas is dropped and a marine is exposed to the agent, dying a gruesome death while the rest of the squad gets out in time. Hummel then occupies Alcatraz Island, taking 81 tourists hostage in the process. Hummel threatens to kill San Francisco's entire population with the VX missiles unless the government agrees to pay $100 million out of a supposed slush fund both to the families of American commandos lost in classified operations throughout the world, and to him and his men.

Captain John Patrick Mason (Connery) is an SAS operative imprisoned for 30 years without trial for stealing microfilm that contained sensitive U.S. Government secrets. Upon his capture, he was disowned by the British government. All evidence of his existence has been erased by both the British and the Americans. An expert escape artist, Mason attempted to escape many times over the years, although he was always recaptured. He has been locked in another maximum security prison for an unspecified length of time since his last escape attempt. FBI Director J. Edgar Hoover had orchestrated all of this, since Mason refused to reveal where the microfilm was hidden, and the policy was continued by then agent, now current FBI Director James Womack (John Spencer). Upon hearing of the VX missile crisis, and after a discussion with Navy SEAL Commander Anderson, Womack reluctantly calls upon Mason, as he is the only man ever to escape from Alcatraz, and he is the one who can guide the commandos into the island via the catacombs underneath it.

Dr. Stanley Goodspeed (Cage), an FBI chemical weapons specialist educated at Columbia (B.A.) and Johns Hopkins (M.A. and Ph.D.) with limited field experience, is placed on the mission as his expertise is needed to disarm the VX missiles.

Mason is summoned by the FBI and agrees to help, only after a "good-faith" conversation from Goodspeed, which will include a pardon, and a stay and haircut at the Fairmount hotel. After tricking Womack into a handshake, Mason throws Womack over the balcony (anchored by a rope) and escapes in a Hummer, leading the FBI and San Francisco police on a wild car chase through the city that causes unaccounted destruction throughout. He contacts his daughter, Jade Angelou (Claire Forlani), that he fathered during his first escape, as she is the only proof of his identity. Goodspeed tracks them down and calls in the police; Jade gets upset and accuses Mason of escaping from prison again, but Goodspeed alleviates her unrest by saying that her father is now assisting the FBI.

Mason, Goodspeed and a team of U.S. Navy SEALs led by Commander Anderson (Michael Biehn) dive underwater and through the catacombs underneath the island. While the SEALs are initially successful in eluding the Marine patrols, they fall into a trap set by marine Captain Hendrix and are surrounded. General Hummel orders the men to surrender but Anderson refuses. The SEALs get nervous during the standoff, which breaks out into a firefight after they are provoked by Captain Frye against Hummel's wishes. Captains Frye and Darrow are part of the renegade marines purely for money and have a disregard for Hummel's code of honor, as Darrow unholsters his sidearm to execute a mortally wounded SEAL, but Hummel waves him away and personally closes the dying man's eyes. Hummel then looks into the fibre optics camera and delivers a stern warning to the FBI, who believe that all hope is lost.

With all of the SEALs killed by Hummel's forces, Goodspeed and Mason find that they are the only ones left between Hummel's VX gas rockets and San Francisco. Mason attempts to desert the mission, but stays after some persuasion from Goodspeed, notably as his daughter Jade and Goodspeed's pregnant fiancée Carla are one of the many citizens that are at risk. FBI Special Agent Ernest Paxton (William Forsythe), who personally advised Goodspeed in good faith, and in charge of the San Francisco region and is focused on the VX gas threat, notices that Director Womack is nervous about Mason taking part in the mission and having no supervision after the SEALs were killed. Paxton finds out that Womack's underlying motive is to recover the microfilm, even if that would have jeopardized the mission. Thus, Paxton understands Mason's anger when he says to Womack: "So you kept this guy without trial his whole life. No wonder he's pissed."

The Marines who are gathering up weapons realize that Goodspeed and Mason remain alive and attempt to bomb them, but they manage to survive. Mason guides Goodspeed through the catacombs to the morgue of Alcatraz. There they fight and kill two Marines stationed there. Goodspeed then defuses twelve VX rockets there by removing their guidance chips so that the rockets will just fall into the sea harmlessly. However, Hummel notes that the morgue team has not checked in and sends a trio of Marines. Mason and Goodspeed take the guidance chips with them and escape on a mine car, but it crashes and Goodspeed is stuck in a belt elevator and Mason hanging from the belt. The Marines arrive and begain shooting at Goodspeed. Mason sets the legs of Marine Captain Hendrix (McGinley) on fire and then drowns him. Goodspeed then tries to flee in the cable car and the Marines follow in another car. Mason surprises the Marines and knocks one of them into the abyss, but he gets choked by another, being saved by Goodspeed who shoots the Marine; Mason deduces that Goodspeed has never previously killed another person.

Hummel then demands over the island's speaker system that Mason and Goodspeed return the guidance chips or they will execute a hostage. Mason smashes the guidance chips, and then tells Goodspeed to disable the three remaining rockets while he surrenders to Hummel to buy time. During the confrontation between Mason and Hummel, both discuss their views on patriotism, and both realize that they are in a similar situation of being betrayed by their respective governments. Nevertheless, Mason tells Hummel that the plan to use VX gas on innocent civilians is insane, to which Hummel has no answer and strikes him. At the same time, Goodspeed is cornered by two Marines and is imprisoned in a cell, as is Mason. However, Mason breaks them out in the same way he got out in 1962. He then decides to abandon the mission, having realized that Hummel is a soldier and does not wish to kill civilians, though Goodspeed says that they cannot take that chance. Goodspeed tries to go on alone but is caught by a Marine sentry, then he is rescued by Mason, who decides to come back.

The Pentagon is preparing to load planes with Thermite Plasma, incendiary bombs, that will burn up the VX gas and also kill everyone on Alcatraz. However, the incendiaries, hot enough to burn the VX poison gas, are still in the testing phase, so it is taking time. There is less than an hour left, and the Pentagon calls Hummel and asks for more time. His remaining men believe it is a trick and urges him to fire one of the two remaining missiles. Hummel bows to their urgings and fires the missile, but at the last moment changes coordinates and sends the missile into the sea. The Marines are furious and wish to know why Hummel changed course. As Mason deduced, Hummel does not wish to kill civilians. (Hummel does subscribe to a code of honor throughout the film of trying not to kill innocents; he used tranquilizers to take out the men guarding the VX in the movie's beginning, and also told his men to cease fire during the firefight with the Navy SEALs.) As the US government essentially called his bluff, Hummel moves to his backup plan to leave the island with four hostages without firing the last missile. However, he is confronted by his surviving men, Captains Frye and Darrow, who openly reveal themselves as sadistic and being part of the mission for money; Hummel made the mistake of trusting Frye and Darrow although they never previously served under him, and perhaps they were not abandoned by the government unlike his other men. A firefight erupts, and Hummel, his loyal right-hand man Major Baxter (Morse) and Sergeant Crisp (Bokeem Woodbine) are killed. Mason and Goodspeed intervene at the last moment and drag the dying General out of the fray, Hummel tells them the location of the last VX missile and dies.

Goodspeed goes out to defuse the last rocket located on the lighthouse. He does so and takes out the VX canisters, but he is cornered by Captain Darrow (Tony Todd). Goodspeed kills Darrow by firing the empty rocket into his direction. Darrow is thrown in the air and is impaled by a pole sticking out of a pile of debris. As Goodspeed goes onto the roof of the lighthouse, he is fired upon by marine Private McCoy (Steve Harris), first with an M249 SAW machine gun and then an M40 rifle. But Mason sneaks up from behind and throws McCoy over the ledge to his death. Mason heads downstairs and is attacked by Private Cox (Brendan Kelly), an Irishman who resents Mason for being English, even though Mason is Scottish as Glasgow was given as his place of birth. Mason kills him by wrapping chains around his neck and throwing them into a nearby well, strangling him.

Unfortunately, the President finally approves of an air strike, and the F/A-18 Hornets carrying the incendiaries are ready and set out for the island, unaware that all the rockets are now defused. Goodspeed is attacked by the last surviving marine, Captain Frye (Gregory Sporleder), but kills him by shoving a VX bulb into his mouth and breaking it. Goodspeed (who has a pronounced fear of needles) saves himself from the exposure by injecting Atropine into his heart. He then sees the approaching jets. He remembers that he was told to set off two green flares when the threat was neutralized. He does so. The flares are seen and the pilots are told to abort their mission at the last second. Before he can disengage the live fire switch, one of the pilots drops a bomb, however, he swerved his aircraft and hit the back of the island, leaving the hostages safe. Goodspeed is thrown into the sea by the explosion but is rescued by Mason. After making radio contact with the FBI, Goodspeed tells Mason that Director Womack tore up the pardon, and so the best thing to do is for Mason to slip away and Goodspeed will say that he is killed. Before leaving, Mason gives him the address to a church in Kansas . Womack is skeptical about Mason's "death", but Goodspeed and Agent Paxton (who knows Goodspeed is lying about Mason's death) move to close the case.

At the movie's end, Goodspeed and his bride, Carla (Vanessa Marcil), are shown just married, fleeing the church with Mason's microfilm as a priest shouts at them for destroying church property.

As their car drives out on the open road, Goodspeed examines the microfilm and says "Honey, want to know who killed JFK?"