Goodspeed is captured before he can disarm the last warhead, while Mason (Connery) meets with Hummel to save the hostages. They are both locked in the cells, while General Hummel waits for the payment to go through before the deadline.
Mason hooks a padlock on some sheets around the door gears to open the cells, and Goodspeed chases after the man to try and convince him to help. He fails.
Goodspeed is soon captured - but Mason shows up to save his life.
The Government miss the deadline. Hummel's men are restless. Responding to their challenges he orders a rocket to be fired at the mainland - but it diverts into the ocean at the last second.
The President responds by ordering an attack on Alcatraz to destroy the warheads.
Hummel's men draw their guns when Hummel and Baxter refuse to deploy the next warhead. The President called their bluff. Shots are fired, and Hummel is badly wounded. With his final breath he tells Goodspeed where the last warhead is located - in the island lighthouse.
Goodspeed removes the toxic chemical cells - but drops one. The soldier Frye appears. They fight. Almost defeated, Goodspeed picks up the chemical ball and slams it into Frye's mouth. He staggers away and stabs the antidote syringe directly into his own heart.
Goodspeed picks up the flares to signal that all is clear - but missiles are fired before the jets can pull up. The compound is hit and Goodspeed is sent flying out into the ocean - to be saved again by Mason.
Before Mason makes his getaway, he tells Goodspeed to take a honeymoon trip to West Virginia or somewhere like that.
The Feds show up. Immediately Womack asks about Mason. Goodspeed tells the old man that Mason was killed.
As it ends, Goodspeed exits a church with the secret microfilm in his hands and jumps into a car next to his bride. He asks if his wife wants to know who really killed JFK!