In January 1994, the U.S. Ohio-class submarine USS Montana has an encounter with an unidentified submerged object and sinks near the Cayman Trough. With Soviet ships moving in to try to salvage the sub and a hurricane moving over the area, the U.S. government sends a SEAL team to Deep Core, a privately owned experimental underwater drilling platform near the Cayman Trough, to use it as a base of operations. The platform's designer, Dr. Lindsey Brigman, insists on going along with the SEAL team, even though her estranged husband Virgil "Bud" Brigman is the current foreman.

During the initial investigation of Montana, a power cut in the team's submersibles leads to Lindsey seeing a strange light circling the sub, which she later calls a "non-terrestrial intelligence" or "NTI". Lt. Hiram Coffey, the SEAL team leader, is ordered to accelerate their mission and takes one of the mini-subs without Deep Core's permission to recover a Trident missile warhead from Montana just as the storm hits above, leaving the crew unable to disconnect from their surface support ship in time. The cable crane is torn from the ship and falls into the trench, dragging Deep Core to the edge before it stops. The rig is partially flooded, killing several crew members and damaging its power systems.

The crew waits out the storm so they can restore communications and be rescued. As they struggle against the cold, they find the NTIs have formed an animated column of water to explore the rig, which they equate to an alien version of a remotely operated vehicle. Though they treat it with curiosity, Coffey is agitated and cuts it in half by closing a pressure bulkhead on it, causing it to retreat. Realizing that Coffey is suffering paranoia from high-pressure nervous syndrome, the crew spies on him through an ROV, finding him and another SEAL arming the warhead to attack the NTIs. To try and stop him, Bud fights Coffey, but Coffey escapes in a mini-sub with the primed warhead. Bud and Lindsey give chase in the other sub, damaging both. Coffey is able to launch the warhead into the trench, but his sub drifts over the edge and implodes from the pressure, killing him. Bud's mini-sub is inoperable and taking on water. With only one functional diving suit, Lindsey opts to enter deep hypothermia and trigger her mammalian diving reflex when the ocean's cold water engulfs her. Bud swims back to the platform with her body; there, he and the crew use a defibrillator and administer CPR, and they manage to successfully revive her.

It is decided that they need to disarm the warhead, which is more than 2 miles (3.2 km) below them. One SEAL, Ensign Monk, helps Bud use an experimental diving suit equipped with a liquid breathing apparatus to survive to that depth, though he will only be able to communicate through a keypad on the suit. Bud begins his dive, assisted by Lindsey's voice to keep him coherent against the effects of the mounting pressure, and he reaches the warhead. Monk guides him in successfully disarming it. With little oxygen left in the system, Bud explains that he knew it was a one-way trip, and he tells Lindsey he loves her. As he waits for death, an NTI approaches Bud, takes his hand, and guides him to a massive alien city deep in the trench. Inside, the NTIs create an atmospheric pocket for Bud, allowing him to breathe normally. The NTIs then play back Bud's message to his wife and look at each other with understanding.

On Deep Core, the crew is waiting for rescue when they see a message from Bud that he met some friends and warns them to hold on. The base shakes, and lights from the trench herald the arrival of the alien ship. It rises to the ocean's surface, with Deep Core and several of the surface ships run aground on its hull. The crew of Deep Core exits the platform, surprised they are not dead from the sudden decompression. They see Bud walking out of the alien ship, and Lindsey races to hug him.

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