An American ballistic missile submarine, the USS Montana, sinks near the edge of the Cayman Trough after an accidental encounter with an unidentified submerged object. As Soviet ships and submarines head towards the area in an attempt to salvage the sub, and with a hurricane moving in, the Americans decide that the quickest way to mount a rescue is for a SEAL team to be inserted onto a privately owned experimental underwater oil platform, the Deep Core, which they will then use as their base of operations. The designer of the platform, Dr. Lindsey Brigman , insists on accompanying the SEAL team, even though her estranged husband, Virgil "Bud" Brigman , is currently serving as the platform's foreman.
As the SEALs and the platform crew attempt to discover the cause of the Montana's failure, they spot strange creatures they cannot identify, later discovering they have intelligence and calling them "NTI's"—"non-terrestrial intelligence." On orders from the SEAL leader Lt. Hiram Coffey and without the platform crews knowledge, the SEALs use one of the platform's mini-subs to retrieve a warhead from a Trident missile aboard the Montana. However, they do so at an inopportune time, as the hurricane strikes the surface and they are unable to detether themselves from the rig's surface support ship the Benthic Explorer. Tossed by the storm, the Explorer's crane and cable system snap off and fall into the water. The crane barely misses the platform when it hits the ocean floor, but fall into the trench, its momentum pulling the whole platform towards the drop off. The rig catches on the very edge of the cliff, preventing a plummet into the depths. Several crew are lost because of flooding in the platform, while the surviving crew and SEALs tend to their injuries and attempt to restore the platform's critical power.
An NTI probe in the form of a living column of water explores the platform, and while the platform crew believe it to be harmless, Coffey sees it as a threat. The platform crew realize Coffey is suffering from high pressure nervous syndrome, which is making him paranoid. Using one of the remote operated vehicles to spy on Coffey from outside the platform, they discover he is planning on sending the warhead down into the chasm to destroy whatever may be down there. Bud attempts to subdue Coffey before he can leave the platform in one of the mini-subs, but he is unable to do so. Coffey is chased by Bud and Lindsey in the station's other sub; they manage to damage Coffey's sub, causing it to fall into the trench, where it is eventually crushed by the pressure and Coffey is killed. However, Bud and Lindsey are too late to stop the remote vehicle and the attached warhead, on a pre-programmed course, from dropping into the trench. Furthermore, their own sub's hull has been ruptured, flooding the sub. Lindsey forces Bud to wear the only diving suit in the sub, while she hopes that the cold water will preserve her body so that Bud can revive her back on the platform. Bud tows her back to the platform, where Bud and the crew are able to resuscitate Lindsey using a defibrillator, and the two reaffirm their lost love.
The crew tracks the warhead, finding the remote vehicle has failed from the pressure and stopped on a ledge partway down the trench. The SEALs have brought with them special diving equipment utilizing a liquid breathing apparatus that would allow for a human to dive that far. Bud volunteers; he will not be able to talk and is instead forced to communicate through a keypad on his suit. Bud begins his dive into the trench, reaching the ledge where the warhead sits, and is guided by the SEALs in disarming it. However, the dive has taken too long for Bud to return back to the top of the trench before the oxygen in the liquid runs out. Bud, aware this could happen and despite Lindsey's pleas to return, decides to remain on the ledge, typing his love to Lindsey in a final message.
As Bud lies on the ledge awaiting his death, bright lights appear below him and he encounters a humanoid NTI. The being reaches out and takes Bud's hand and then leads him even further down to a massive craft sitting deep in the trench. Taken deep within the ship, the NTIs provide Bud with an atmosphere for him to breathe, followed by showing him his typed, last messages of self-sacrifice and devotion that he had sent to his wife.
On the platform, believing Bud to be dead, Lindsey and the crew are surprised to find Bud replying back to them, telling them to get ready. The crew observe something very large quickly rising out of the trench, and see the lights from the NTI ship as it rises. The enormous ship eventually surfaces, lifting many of the naval ships out of the water and leaving them aground on the NTI ship's hull, as well as the platform itself. Leaving the platform on the surface of the ship, the platform crew and remaining SEALS are surprised to find they are fine and not suffering from decompression sickness after rising so fast out of the water, believing it to be an effect by the NTIs. Bud emerges from the NTI ship, and he and Lindsey rush to meet each other, engaging in a passionate kiss.
Special Edition
The special edition includes more of the conflict between the United States and Soviet forces over the crash of the
Montana, each side initially blaming the other for the disaster. When Bud arrives on the NTI ship, he is shown images of humanity's destructive behavior on a view screen. The NTIs create enormous megatsunami-level waves that threaten every coastline, including New York City and San Francisco , but then stall them moments before they would come crashing down. After showing Bud his messages of self-sacrifice and caring and believing humanity to be capable of the same, the NTIs cause the standing waves to harmlessly recede back to normal ocean levels, after which they start to bring their ship to the surface.
Despite the fact that James Cameron had final cut on the original theatrical version and almost all cuts were decided by him, the extended version is often mislabeled as a "director's cut".
