The story unfolds as the American battleship USS Missouri (BB-63) arrives at Pearl Harbor. In a moment of national pride, President George H. W. Bush delivers a speech announcing that this proud vessel, after years of service, is set for decommissioning in California, marking its final journey. Casey Ryback (Steven Seagal), the ship's Chief Petty Officer and cook, is busy preparing a festive meal to celebrate Captain Adams' birthday, much to the chagrin of his rival, Commander Krill (Gary Busey). Krill has arranged for lavish food and entertainment to be airlifted from Hawaii, a direct challenge to Ryback’s efforts.
Tensions boil over when Krill instigates a skirmish in the galley, leading to Ryback assaulting him. However, Krill cleverly retaliates by locking Ryback in a galley refrigerator and assigning the dim-witted Marine, Private Nash (Tom Wood), to keep watch. Their situation becomes dire when a CH-46 helicopter touches down, bringing not just a band and Miss July '89 (Erika Eleniak), but also a crew of mercenaries led by ex-CIA operative Bill Strannix (Tommy Lee Jones). Strannix, masquerading as the band leader, swiftly reveals his true intentions by eliminating Commander Green, the ship's highest officer.
With Krill's treachery uncovered, the mercenaries seize control of the ship, leading to the deaths of several crew members, including the captain. Strannix’s plan is to commandeer the ship's nuclear arsenal and sell it on the black market, while Krill assists in the takeover. Amidst chaos, Strannix's team executes a plan to strike Honolulu, aiming to erase tracking systems during their escape.
Meanwhile, Ryback realizes something is amiss after hearing gunfire and urges Private Nash to notify the bridge. However, Krill neglects to notice that Ryback is still in the galley and concocts fabrications to downplay the situation. Strannix, not wanting to leave Ryback unchecked, sends mercenaries Cates and Ziggs to silence him. In a tense sequence, Ryback manages to escape his confines, taking out Cates and strangling Ziggs, all while setting a bomb in the microwave.
As the battle intensifies, Ryback showcases his combat expertise, aided by Jordan and a handful of crew members who have eluded capture. Utilizing his covert training, Ryback contacts Admiral Bates (Andy Romano) at the Pentagon, triggering a strategic response that involves deploying a SEAL team to regain control of the Missouri. However, Krill's awareness of Ryback's credentials complicates matters, revealing his true nature as a highly trained former Navy SEAL, unjustly assigned to the kitchen.
To further their evil plan, Krill sets a trap to drown the remaining crew, anticipating Ryback’s solo rescue attempt. But with cunning, Ryback rallies the hidden sailors, successfully counteracting the ambush. He skillfully disables the Missouri’s weapon systems to allow Navy SEALs to approach, even as Strannix prepares a counteroffensive against incoming help.
Just as the climax escalates, Strannix executes a dangerous strategy of launching missiles toward Honolulu, forcing the Pentagon to authorize a preemptive airstrike on the Missouri. Ryback, with assistance from Jordan, ultimately triggers a showdown with Strannix, during which old rivalries surface, revealing a shared covert past. Their confrontation leads to a harrowing struggle, ending in Ryback's favor as he defeats Strannix, secures the launch codes, and averts a major disaster by deactivating the remaining missile.
As the dust settles, the Missouri’s crew is finally liberated, the ship sailing towards San Francisco harbor. A touching reunion ensues, highlighted by Ryback's affection towards Jordan amidst cheers of the crew. The film concludes with a solemn yet proud tribute, honoring Captain Adams in a heartfelt funeral on deck, as Ryback stands tall, saluting the fallen comrade with respect and recognition for their shared sacrifices.
