The film begins with the downing of a US nuclear submarine: US Montana, after the submarine is struck trying to evade a fast moving, unidentified underwater object.
Our first sight of Lt. Hiram Coffey comes when he and his Navy SEAL team arrive by Navy helicopter onboard the support vessel for an prototype underwater oil-drilling and exploration platform called Deepcore. The project engineer of the platform, Lyndsey Brigman, arrives with them.
The rig foreman, Bud Brigman, is informed that the Navy has asked them to join the rescue attempt for the downed submarine, offering danger money to the civilian divers. Lindsey pilots the minisub containing herself and the Navy SEAL team down to Deepcore, and we discover that she and Bud are separated awaiting final divorce. The new arrivals have to wait in decompression chamber for several hours to acclimatise their bodies to the underwater pressure. This is where Lindsey first mentions watching signs for HPNS: High Pressure Neurosis Syndrome, giving a list of symptoms... Coffey ends the list with 'and a partridge in a pear tree'. He tells her that they know all about HPNS but that they have all worked this far underwater before with no problems. Lyndsey tries to stress that it makes no difference if this is their first time or hundredth as HPNS can strike at anyone.
When finally released from the decompression chamber, Coffey and his team of three other SEALS go straight to the pool to prepare the necessary equipment for boarding the Montana. When he goes back to get the last of the equipment, he notices that his hand is trembling - the first sign of HPNS.
Coffey explains to the civilian divers the plan he has drawn up for entering and searching the US Montana for survivors. One of them baulks at the idea of going into a damaged nuclear submarine and Coffey reacts rather more aggressively than he ought to have. Increased aggression and sense of paranoia being another symptom of HPNS. Privately, Bud Brigman tries to explain to Coffey that he has to treat the civilians with a little more care but Coffey ignores him.
The divers head for the wreck of the US Montana, and enter the stricken submarine. They start the search but every compartment they come across has been flooded. Coffey goes to the Captain's safe to retrieve the Crypto book holding all the codes for the nuclear warheads carried onboard the submarine. In the meantime, one of the civilian divers, Jammer, sees something that sends him into a catatonic shock.
Fearing that this unidentified object that shocked one civilian and was witnessed by Lindsey could be some ultra-modern Russian device, Coffey requests additional orders from his Navy superiors. Although there is a heavy storm brewing topside (hurricane) Coffey obeys his orders and the SEALs return to the submarine to retrieve a warhead. By the time they get back with flatbed it is too late for One Night to release the cable connected them to the support ship above. The crane has buckled under the strain of the high seas and is falling. Everyone braces for impact.
The crane lands about twenty feet in front of Deepcore and every cheers until it starts to slide into the Abyss of the Cayman Trench, dragging Deepcore with it. Deepcore is severely damaged, with civilians killed when trapped in flooding compartments. Brigman is saved by the titanium wedding band he still wears despite his estrangement from Lindsey as it prevents the door from closing on him. Catfish rescues him by cutting the hydraulics to the door to allow them to pull it open enough for him to reach safety.
Coffey tries to apologise to Brigman, saying he is sorry but that he was under orders. It is obvious that he takes his duty to his job - and to his superiors - very seriously.
The survivors have a meeting but none of the civilians are willing to follow any order Coffey gives as they blame him for the deaths of their colleagues and their dangerous predicament. Brigman intercedes and persuades them to do as Coffey as ordered.
Coffey goes back to his quarters and, with another SEAL, he starts work on arming the warhead. However, Alan 'Hippy' Carnes sends 'Little Geek' to look through the port and when Lindsey finds out they have brought a nuclear device onboard her rig, she goes ballistic and confronts Coffey. Brigman's quick thinking prevents the confrontation from getting too ugly and he drags Lindsey away from Coffey. He explains to her that Coffey is showing all the signs of HPNS and must be considered dangerous so it was wise not to provoke him.
NOTE: As the camera pans on Coffey's back during the confrontation we see that Coffey is holding a gun at the small of his back, ready to deal with Lindsey permanently, if necessary. Later, Coffey uses the internal monitoring equipment to overhear the civilians discussing him.
Everything settles down for a while until a strange snake-like column of water rises from the pool and travels through the habitat. Lyndsey wakes up and, awakens Bud Brigman. The 'water' seems sentient, morphing into their faces and Lyndsey touches it, discovering that it is composed of sea water. They follow it as it winds through the ship until it comes to the room where Coffey has the warhead. Coffey arrives, sees what it is looking at and slams the hatchway closed to chop off part of the 'creature'. It seems to turn on him and he shrinks away in fear, but it doesn't attack. Instead it flows back to the pool and disappears.
The survivors meet to discuss what they have seen and Lindsey makes snide asides aimed at Coffey. He glares at her and looks uncomfortable, and then the camera pans beneath the table where we see he is methodically mutilating himself with a series of slashes across his left forearm.
When Hippy snoops around, trying to see what Coffey is up to, he is surprised when Coffey comes up behind him silently. Coffey looks extremely close to the edge of full-blown paranoia. He orders all the civilians into a single place and sets two of his SEALs to guard them.
One of the guards is overpowered when Jammer wakes up from his catatonic coma, and Brigman and Catfish race off to find a way to stop Coffey from sending the armed and primed nuclear warhead down the Abyss to destroy the aliens. They swim part way but Brigman has to go the remainder of the way alone.
When he reaches the pool, he spots Coffey sitting on a bench playing with the chains of a winch. The warhead has been strapped to 'Big Geek' but Coffey seems frozen in place as if he is trying to sort out the thoughts in his head. Brigman tries to sneak up behind him but Coffey's SEAL trained senses have him spinning, aiming the gun at Brigman. He pulls the trigger but it is empty.
Back in the 'monitor' room, Monk shows the others the clip he palmed from Coffey's gun earlier and proves he is on the side of the civilians in the belief that Coffey is sick and needs to be relieved of command.
Coffey and Brigman fight with Coffey's superior fighting skills giving him the edge right until Catfish arrives and knock his down with a punch. Coffey leaps into the water, swims and then climbs into cab3. Brigman tries to stop him and manages to tie off 'Big Geek' but only temporarily. Lindsey pilots flatbed and goes after Coffey, bringing Brigman onboard. There is an underwater dogfight between the two minisubs but Lindsey finally gets the upper hand and rams Coffey's sub.
They stare at each other through the two layers of dome and there is a moment of sanity and realisation that passes between them before cab3 slips over the edge of the Abyss. Without any means to halt its descent, it gradually reaches the maximum pressure tolerance level. The dome cracks and then implodes, destroying cab3 and killing Coffey.
Remainder of film:
Brigman has to watch Lindsey drown as their own sub fills with water, He drags her back to Deepcore and, with assistance from the others, they manage to revive her. Brigman realises that someone has to go into the Abyss to prevent the nuclear device being detonated. He agrees to wear a special suit that uses a liquid oxygen mixture to enable divers to go far deeper. Brigman ascends into the Abyss, and we watch as Bud and Lindsey become fully reconciled as husband and wife as Brigman's mental faculties deteriorate due to the increased pressure of water upon him.
He locates 'Big Geek' and disarms the warhead. There is not enough oxygen left for him to get back. Lindsey is distraught but Brigman tells her he knew it was a one-way ticket when he accepted the task. He decides to stay where he is rather than try to climb.
A strangely illuminated creature - just like the one Lindsey spotted earlier - finds Brigman and takes him to its 'home'. The water pulls aside like a curtain and Brigman removes the helmet - which is depleted of oxygen by now anyway, and realises he can breath; that they have made him an air-filled chamber. He converses with the aliens and discovers that they were about to destroy all human life using huge tsunamis because humans are so destructive and cruel, but have changed their minds after watching his show of courage and the love he held for his wife.
The sentient creatures bring there whole city up to the surface, with Deepcore on it. No one needs decompression and the world has learned that it is no longer the only sentient beings on the planet.