Text appearing in red describes footage from the 1993 Special Edition of the film.
, a U.S. Navy nuclear missile submarine, operating deep in the Cayman Trough in the Caribbean Sea, encounters an unidentified submerged object moving at high speed. The object passes very close to the submarine and the vessel loses power. Power is restored after a few moments, however the sub has drifted too close to the underwater canyon wall and collides with it, causing catastrophic damage. An officer is able to launch the sub's emergency beacon before the sub floods, drowning the entire crew.
As Soviet ships and submarines head toward the area in an attempt to salvage the sub and its, and with a hurricane moving in, the Americans decide that the quickest way to mount a rescue is for a US Navy SEAL team to be inserted onto a privately owned experimental underwater oil drilling platform, which they will then use as their base of operations. The platform's designer and chief engineer, Dr. Lindsey Brigman (Mary Elizabeth Mastrantonio
), is furious at the notion of her rig being commandeered for the mission. Her estranged husband, Virgil "Bud" Brigman (Ed Harris
) is the foreman of the platform. However, Benthic Petroleum, the rig's financier, has already agreed to cooperate with the Navy and has promised the rig's crew substantial bonus pay. Lindsey herself travels down to the rig with the SEAL team to oversee the operation personally. After eight hours in a compression chamber, Lindsey and the SEAL team emerge; no one, however, sees that SEAL leader Lt. Hiram Coffey (Michael Biehn
) has developed High Pressure Nervous Syndrome (HPNS) when he has a slight hand tremor. Lindsey and Bud promptly begin arguing with each other, revealing that they are a separated married couple. Bud becomes furious and throws his wedding band into a chemical toilet. He relents after a few moments and fishes it out, staining his hand blue with the toilet's sanitation fluid.
The rig and SEAL teams prepare to investigate the submarine wreck. One of the SEALs shows crew members Hippy (Todd Graff
) and Catfish (Leo Burmester
) a high-tech underwater breathing system that uses oxygenated fluid instead of air. The system allows its wearer to survive at extreme ocean depths without succumbing to the intense water pressure. Coffey himself leads the entire operation, issuing orders and angrily reprimanding the crew when they begin joking with each other.
While searching the sub for survivors, the collective team encounters strange creatures they can't identify, the same beings that inadvertently caused the submarine to sink. Lindsey, piloting one of the rig's three mini-subs, experiences the same type of power loss that the Montana
did. While searching a compartment on the Montana
, Bud's partner, Jammer (John Bedford Lloyd
), the rig crew's biggest member, sees a strange, glowing creature and panics. When he tries to escape the chamber, he damages a valve on his breathing apparatus and begins to convulse. Bud and his comrades are able to save Jammer, but the incident puts him in a coma.
As the storm intensifies, Coffey and his team communicate with their commanding officer on the surface, who tells them that a Russian attack sub was detected in the area. The team is ordered to retrieve a Trident missile warhead and arm it as a contingency if the Russians get too close to the Montana.
Coffey and the SEALs take one of the rig's mini-subs without authorization. Using the sub's large mechanized arm, they are able to open a launch door of the Montana and extract one of the Tridents.
. However, the mini-sub they commandeered 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 pilot, "One Night" (Kimberly Scott
), 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 Cayman Trough. 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 sees that the crane's momentum will pull the rig into the chasm, and they brace for the impact. The station is violently yanked towards the chasm causing massive damage and flooding, killing six of the station's crew one of the SEAL team and injuring several of the surviving crew and SEALs. The rig is not pulled into the trench, stopping a few feet short of the precipice.
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 by Hippy), which the paranoid Coffey determines to be a threat. While activating oxygen tanks outside the rig, Lindsey encounters one of the smaller probes she'd spotted while at the submarine & then a much larger and brilliantly illuminated vehicle which she touches. As both vehicle sputter out of sight into the chasm, she is able to get a few pictures.
Another incident involves an encounter with a tentacle that appears to be made entirely of water, but can move like a snake. It also morphs into the faces of both Lindsey and Budd in an apparent attempt to communicate. When Coffey finds the tentacle's origin in the rig's diving pool, he panics and closes one of the hatches, cutting it off, and the remainder sinks into the depths. When the end of the tentacle "looks" at him, Coffey becomes even more scared and paranoid.
Strapping the warhead to Big Geek, one of the platform's remote operated vehicles, Coffey makes a fateful decision to send both of them down to the bottom of the trench where the NTIs appear to be coming from. He dogs and jams the door to the rig's sub bay and waits until it's time to launch Big Geek. Due to the damage caused to the rig, Bud and Catfish have to swim to the sub bay under the rig in freezing cold water. Bud makes it to the bay, having to leave Cat behind at another hatch. Bud tries to sneak up on Coffey with a large pipe but decides to grab the pistol Coffey had tucked into his belt. Coffey spots him and tries to shoot Bud but the pistol is empty: one of his SEAL team, Monk, had previously unloaded the pistol. Bud and Coffey fight hand-to-hand with Coffey finally wrapping a cable around Bud's neck. Suddenly, Cat appears and punches Coffey in the face, knocking him on his back. Coffey retreats to the sub and escapes, moving into a position where he can launch Big Geek.
Bud and Lindsey intervene; Bud ties the runaway ROV to a railing on the rig and is picked up by Lindsey piloting one of the rig's subs. After a furious chase along the sea bottom, Lindsey disables both subs and stops Coffey, who falls off the edge of the trough and is crushed within his submersible by the pressure. However, they cannot stop the ROV from taking the warhead down into the trench. Trapped in their rapidly-flooding sub, 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. A very tense situation develops while her comrades try to resuscitate her. When using emergency equipment fails, Bud frantically begins to shake and even slap Lindsey, who regains consciousness, much to the relief of the entire crew.
Being the most qualified and strongest diver left, Bud then dons an experimental diving suit given to him by the remaining SEALs, in which the diver breathes an oxygenated 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, two miles down and 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 rig. He tells her, via a wrist keypad, 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, an immense, glowing city. They provide him with air to breathe at his normal pressure and engage in silent communication with him. They then 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. They also show Bud a few current newscasts of an incredible phenomenon along continental coasts on the surface. The NTIs are using their ability to control water to form 1000' high tsunamis off the coasts of every continent on Earth, threatening to destroy humanity. Bud asks the NTIs what right they have to judge the human race. He is shown historical clips of Hitler, war, and genocide.
However, when the The NTI's had intercepted Bud's transmission "LOVE YOU WIFE" they decide to stop the storm and tsunamis, realizing humans do possess compassion for each other.
Back on the rig, everyone is saddened by the loss of Bud. However, they pick up a typed message from Bud telling them that he's alive and well and that they should brace themselves. The NTIs raise their entire city from the chasm, but it is so massive it lifts most of the naval fleet patrolling the area above the water, including the Explorer. The rig is also on the city and everyone seems fine, including the underwater crew, who should have died without decompressing -- 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.