The film begins with the American battleship USS Missouri (BB-63) arriving at Pearl Harbor, where President George H. W. Bush makes a speech announcing that after the Missouri's long time service, the ship will be decommissioned in California, making the trip her final voyage. Casey Ryback (Steven Seagal), a Chief Petty Officer assigned as cook, is preparing meals in celebration of the birthday of Captain Adams (Patrick O'Neal), against the orders of his adversarial Executive Officer, Commander Krill (Gary Busey), who is having food and entertainment brought from Hawaii by helicopter after they have set out to sea. Krill provokes a brawl in the galley with Ryback who assaults Krill. Unable to imprison him in the brig without clearance from the captain or attracting attention, Krill detains Ryback in a freezer and places a Marine, Private Nash (Tom Wood), on guard to prevent Ryback from leaving. A CH-46 helicopter lands on the ship's deck with a musical band, along with Playboy Playmate "Miss July '89" Jordan Tate (Erika Eleniak) and a group of caterers who are all really a band of mercenaries led by ex-CIA operative Bill Strannix (Tommy Lee Jones). Shortly after the party begins, Strannix, posing as the band leader (Bad Billy and the Bail Jumpers), pulls out a gun and kills Commander Green (the highest ranking officer in the room). Then, all the caterers and band members pull out weapons to seize control of the ship with the help of Commander Krill (who is revealed to be a turncoat). Several of the officers are killed during the takeover, including Captain Adams, who is shot point blank by Krill. The rest of the ship's company are imprisoned below decks in the forecastle, except for several stragglers in secured areas.Strannix intends to steal the ship's arsenal of nuclear Tomahawk cruise missiles and plans to sell the nuclear weapons on the black market by unloading them onto a submarine Strannix stole from North Korea while on his final CIA mission, which he then kept for himself when the CIA tried to assassinate him to use for private arms trading. Strannix and his men take over the ship's weapon systems for defense, shooting down an F/A-18 Hornet sent to investigate, and plan on covering their escape by launching a missile strike into Honolulu that will obliterate tracking systems in Pearl Harbor.Ryback has become suspicious upon hearing gunfire and tells Private Nash to contact the ship's bridge. An annoyed Krill realizes they forgot about Ryback in the freezer and learns the kitchen is an unsecured area on the ship. Krill lies to Private Nash that the noises were not gunshots, but party poppers before Strannix offhandedly sends mercenaries Cates and Ziggs to eliminate Ryback and Nash. Nash is killed, but Ryback escapes and kills Cates by throwing a knife at him and strangles Ziggs, then plants a bomb in the microwave to go off later. He proceeds to cause havoc amongst the perpetrators and begins killing off the terrorists with the limited help of Jordan Tate, who was only hired as a cover for the festivities. Ryback also gets in contact with Admiral Bates (Andy Romano) at the Pentagon by using a satellite phone, whereupon the Navy then makes a plan to send a SEAL team to retake the ship. Krill discovers that Ryback is really a Chief Petty Officer and former Navy SEAL with extensive special-weapons and counter-terrorism training. He was relegated to his current posting for striking his superior officer who had been responsible for his men being killed in a botched commando mission during the United States invasion of Panama. As a result, he had lost his security clearance and was only able to serve as a yeoman or a cook. To keep the missile-theft plan in place, Krill decides to activate the fire sprinklers in the forecastle, leaving the crew members to drown and the terrorists to set up an ambush when Ryback arrives, presumably by himself to save them. However, Ryback locates a group of sailors in hiding and along with them engages a successful counter-strike, turning off the sprinklers dousing the crew and eliminating a considerable number of Strannix's forces. As Strannix's men regroup, Ryback shuts down the Missouri's weapon systems, in order to allow the incoming Navy SEAL team to land.As the battle for the ship continues, the submarine crew shoots down both the CH-46 helicopter carrying the Navy SEAL team with shoulder-fired surface-to-air missiles. The Pentagon responds by ordering an air strike that will sink the Missouri and all aboard. Strannix regains control of the ship's weapon systems and the Tomahawks are loaded onto the North Korean submarine, departing with Krill on board. With the aid of Jordan and his fellow sailors, Ryback uses the battleship's guns, which were not yet decommissioned, to sink the submarine with Krill still inside, killing him and every one on board.Strannix, standing on the deck, suffers a major concussion from being in the proximity of the Missouri's guns as they are fired. He orders the remaining mercenaries out of the control room as he launches two nuclear-tipped Tomahawks towards Honolulu. As the sailors recapture the ship, killing the last group of Strannix's men, Ryback finds his way into the control room where he is caught off-guard and captured by Strannix. Strannix and Ryback realize they know each other from their past covert experiences, but Ryback is disgusted by Strannix's excuses for his behavior. Ryback states that both of them are disillusioned and were essentially "used" by their government, but Strannix says Ryback still believes in his country, whereas he does not. Ryback and Strannix then engage in a knife fight wherein Ryback kills Strannix by poking his eye out, stabbing him in the head with his knife, and finally smashing him through a computer monitor. Ryback then takes the launch codes needed to self-destruct the Tomahawk missiles. One of the two missiles is destroyed by an F/A-18 Hornet, but the other continues on its course. The codes are dialed in and the Tomahawk missile is deactivated, blowing apart before it would have destroyed Honolulu. The Pentagon celebrates wildly, then calls off the air assault on the Missouri.At the end, the remaining crew members are freed from their forecastle prison as the ship sails towards San Francisco harbor. Ryback is checked by a Navy doctor, kisses Jordan and the crew looks on and cheers. The film ends with a funeral ceremony for Captain Adams being held on the decks of the Missouri, showing the Captain's casket with flag draped over it and Ryback saluting in his service dress blue uniform with his full rank and military decorations.