In May 1968, Captain Dmitri "Demi" Zubov (Ed Harris), a seasoned but troubled veteran of the Soviet Navy, finds himself facing the twilight of his career that stands in the shadow of his illustrious father. He is tasked by Admiral Markov (Lance Henriksen) to commandeer an aging submarine, a vessel that Demi once masterfully led early in his service, poised for one last journey before its handoff to the Chinese.
Despite returning from a grueling 76-day cruise and anticipating a well-deserved three-month furlough with merely three weeks in the docks, Demi is overridden by Markov, who presents this mission as a fitting farewell to the venerable captain from the Navy. The backdrop to this honor, however, carries heavy burdens, as Demi grapples with the haunting memories of a past incident where six individuals perished under his command during a tragic mishap involving collision and fire.
Demi disrupts a lively party among his crew, including the promising Alex Kozlov (William Fichtner), who is readying himself for greater aspirations in his career. As they set sail, joined by Bruni (David Duchovny) and his cadre of technical experts testing a prototype apparatus, ominous signs emerge. Demi hears unsettling sounds reverberating through the submarine, yet an external search yields no clues. Tension escalates as Alex uncovers Bruni's lack of a legitimate record in the navy, suggesting a possible connection to KGB radicals or commandos. The political officer on board, Pavlov (Johnathon Schaech), adds to the growing unease among the crew.
As fate would have it, the submarine finds itself pursued by an American attack sub. In a bid to evade detection, Demi and Alex uncover their initial orders directing them to a designated ocean region to test the prototype. However, complications arise when Bruni begins shifting the mission's objectives, straining Demi's patience as he demands the submarine to draw dangerously close to a merchant ship, putting the mission and their lives at risk.
Through a series of heart-stopping maneuvers, the true nature of Bruni's mission comes to light: he aims to employ a device known as the Phantom to disguise their vessel’s acoustic signature, masquerading it as a civilian ship or others in the vicinity. When confronted by Demi, Bruni's aggression escalates to the point where he publicly discredits Demi’s competency, citing past failures and accusing him of unfitness for command.
Confined and desperate, Demi recounts the traumatic past where he faced a fire onboard, forced to seal compartments to save the remaining crew, a haunting event that led to his current struggles with epilepsy and seizures. The stakes collide as Bruni pressures Alex to disable the nuclear warhead aboard the submarine, prompting Demi, Kozlov, and other loyal crew members to brainstorm a desperate plan to reclaim control of the vessel.
Communicating their plight to a nearby Soviet submarine, a thrilling sequence unfolds as they fashion a transmitter to signal their distress. In a dramatic revelation, Bruni admits that he and his operational team are rogue agents, driven by fears of a U.S. military initiative called "Dark Star," designed to cripple Soviet nuclear capabilities, which threatens their homeland.
Surrounded by danger, Demi ultimately eludes torpedo strikes from the K-123 submarine and orchestrates a counterattack, only to find themselves enmeshed in a perilous ruse meant to trigger a nuclear war between the United States and China. As they grapple for control over the submarine, the plot thickens with violent confrontations resulting in casualties among both sides.
As the submarine suffers devastating damage and descends into the depths of the ocean, a harrowing struggle ensues for survival against the lethal gas filling the confines of the ship. With herculean effort, Alex launches a rescue attempt, all while Bruni reveals he was complicit in the previous tragic fire that claimed lives under Demi's command.
Eventually, the remaining crew is recovered, and stricken yet heroic, they stand atop the submarine as a specter of their former selves. Demi's wife and daughter express admiration for his valiant actions from the dock, while Alex, now a captain, offers a salute to his fallen mentor. In a poignant twist, the men, now mere phantoms, observe from beyond as the Americans salvage the unscathed warhead from the ocean depths, leaving the specter of conflict and sacrifice lingering in the watery abyss.
