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, which they will then use as their base of operations.
In a subplot the SEAL team is accompanied by the platform's designer, Dr. Lindsey Brigman (Mary Elizabeth Mastrantonio). Her estranged husband, Virgil "Bud" Brigman (Ed Harris) is the foreman of the platform. Unbeknownst to anyone, the Navy SEAL leader Lt. Hiram Coffey (Michael Biehn) has developed High Pressure Nervous Syndrome, and is losing his ability to reason as he passes slowly into a paranoid state.
As the oil workers and SEAL team investigate the wreck, the workers have strange encounters with a creature they can't identify, the same being that inadvertently caused the submarine to crash. Meanwhile, the estranged Brigmans argue a great deal; yet underneath, they clearly have affection and respect for one another.
As the storm intensifies, Coffey and his team take one of the rig's mini-subs without authorization on a classified mission to the Montana to retrieve one of the warheads from the ship's Trident missiles. Unbeknownst to the SEAL team, the mini-sub that they took was the only vehicle capable of disconnecting the station's umbilical cord to its parent surface ship, the Benthic Explorer. Upon their return, the SEALs remove the warhead and turn the sub over to its normal pilot, "One Night", who takes it out in an attempt to disconnect the umbilicus.
By this time, the Explorer is in the middle of the hurricane, and being tossed violently by powerful winds and waves generated by the storm. The ship's motion makes it impossible for One Night to disconnect the cable, which is jerking about with such power that it begins to drag the station along the bottom towards the trench. The stress of the cable causes the derrick crane that supports the station to break away from the ship, momentarily stopping the station's slide towards the trench. The crew is relieved that they have avoided death, but the joy is short-lived as they realize the crane, which is still attached to the rig via the umbilicus, is descending to them at an increasing rate. As it floats past the rig into the chasm, the crew realizes that the crane's momentum will pull the rig into the chasm, and they brace for the impact. The impact violently jerks the station towards the chasm causing massive damage and flooding, killing six of the station's crew and injuring several of the surviving crew and SEALs.
Tensions mount as the platform has lost contact with the surface and anger of the crew towards the SEALs intensifies over the deaths of their friends and co-workers. The crew begins to experience more strange encounters from what appear to be underwater beings (referred to as non-terrestrial intelligences, or NTIs), which the paranoid Coffey determines to be a threat. Strapping the warhead to Big Geek, one of the platform's remote operated vehicles, he decides to send both of them down to the bottom of the trench where the NTIs appear to be coming from. Bud and Lindsey intervene and manage to stop Coffey, who falls off a ledge and is crushed within his submersible by the pressure, but are unable to stop the ROV from taking the warhead down into the trench. Trapped in a rapidly-flooding submersible, Lindsey orders Bud to use the ship's sole diving suit to swim back to the platform, towing her body. While she will drown, she banks on the very cold water preserving her via the mammalian diving reflex until she can be resuscitated in the platform. Bud complies and manages to save her life, using a defibrillator.
Bud then dons an experimental diving suit given to him by the remaining SEALs, in which the diver breathes in a special fluid instead of air. This has the advantage of allowing the diver to descend to incredible depths without injury, as the body will not be crushed by the pressure by having liquid in the lungs rather than gas. Bud's mission is to dive to the bottom of the trench, deeper than anyone has ever gone before, and disarm the warhead before it detonates. He succeeds in his mission, but Lindsey is distressed to learn that he does not have enough breathing fluid remaining to allow his return to the platform. He tells her, via a wrist pad, that he always knew it was a one-way trip, but that he had to go to save both the platform crew and the NTIs. He transmits a final message saying that he loves her and still considers her to be his wife, and she tells him how much she loves him before assuming he's dead.
The NTIs find Bud as his oxygen runs out and bring him onto their ship. They provide him with air to breathe at his normal pressure and engage in silent communication with him. They then proceed to show him several Television clips they have stored of humanity's destructive behavior, silently explaining that they have left humans alone but now believe humans are too self-destructive to continue this behavior. The NTI's view Bud's transmission "Love you Wife" and decide to stop the storm and tsunamis, realizing human compassion. With everyone baffled, Bud types another message into his communicator and tells them what he has discovered. The NTIs proceed to surface their underwater ship, but it is so massive it lifts most of the naval fleet patrolling the area above the water, including the explorer. Everyone seems fine, including the underwater crew without any need to decompress as the NTI's altered their bodies to allow this. Lindsey sees Bud emerge from the NTI ship and they rush to each other. Greeting each other as a newlywed couple would, they engage in a passionate kiss.
