In the near-future, the intercontinental corporation, Tri-Oceanic Corp., has hired a crew of undersea miners to do a 90-day mining operation on the bottom of the Atlantic Ocean. The head of the corporation, Miss Martin (Meg Foster), hires Steven Beck (Peter Weller), a geologist, to assist in mining operations as well as command the undersea mining station. In addition to Beck, the eight-person crew consists of Dr. Glen 'Doc' Thompson (Richard Crenna) the research specialist and local physician; Elizabeth 'Willie' Williams (Amanda Pays), a female miner; Buzz 'Sixpack' Parrish (Daniel Stern) a brash miner; Justin Jones (Ernie Hudson) a good-natured miner; Tony 'DeJesus' Rodero (Michael Carmine) another miner and mechanic; Bridget Bowman (Lisa Eilbacher) a maintenance worker and computer expert; and G.P. Cobb (Hector Elizondo) an older miner and multi-task maintenance man.
While outside their vessel in a pressure suit during a routine drilling, Sixpack trips and stumbles upon a wrecked cargo ship. Because he didn't respond to hails over his radio, Williams goes to look for him and finds him excited over "treasure." From Williams' video camera feeds, Dr. Thompson, sees that it is a Russian ship and identified the ship as the "Leviathan" from it's markings. When checking on records of Leviathan, the crew discover that it is still marked as an active ship on duty in the Baltic Sea.
After Williams and Sixpack return from the wreck, the rest of the crew open a safe from The Leviathan that Sixpack took and find several crew records relating to deceased crew members, as well as a video tape from the captain of Leviathan. Among the materials, Sixpack finds a flask of Vodka. There being no alcohol on their underwater base, he hides this for his own use later. Bowman figures out Sixpack had hidden away the Vodka and persuades him to share it.
That night, Dr. Thompson and Beck review the videotape of the Russian captain of Leviathan and believe his medical log was cryptic over the crew's poor health condition. The Russian captain describes his infirmary filled with sick crew members which the ship doctors tell him that it may be a "tropical infection" or "plague" infecting the ship and that "something's off" before the tape suddenly ends. They also look through the video images from Williams' camera of the Leviathan and noticed a large hole in the hull which was possibly hit by a torpedo.
The following morning, Sixpack awakes feeling sick, with lesions throughout his back. The Doc Thompson is unable to offer any explanation for why Sixpack ended up like this. He asks the computer for an opinion, and it responds with a "guess", suggesting "genetic alteration." Sixpack dies eight hours after first feeling sick, but the doctor and Beck hide news of his death to avoid a panic amongst the crew. Dr. Thompson carries out routine medical checks to make sure no one else is sick, but doesn't have the chance to examine Bowman.
While Beck and Dr. Thompson have a video conference with Ms. Martin (on the surface), Bowman has already began to feel the effects just like Sixpack. She becomes emotionally distraught when she begins losing hair. She accidentally stumbles upon Sixpack's corpse and witnesses it mutating right in front of her.
Meanwhile, Beck and Dr. Thompson don't want to take risks and ask Martin to execute an emergency medical evacuation. Martin makes the excuse that the evacuation will happen, but there is a possible severe storm on the surface which will hamper efforts, and may delay things for another 12 hours.
Dr. Thompson finds Bowman. Unable to cope with the idea of dying like Sixpack, she has committed suicide by slitting her wrists in the shower. Her body is taken to sickbay, where Beck and Thompson find Sixpack's body mutating. They decide to dump both bodies without the crew's knowledge. As they are about to "flush" the bodies, the crew try to open the bag as they see the mutating corpses writhing through the body bag, and believe someone was alive inside.
The creature that is forming inside attacks and claws Cobb before they succeed in ejecting the body. The surviving crew are finally informed of what has happened and realize that the Leviathan (ship) was experimenting with mutagens to the unknown crew. Dr. Thompson speculates that Soviet Russian scientists tainted the crew's vodka with live mutagen cells which made the crew members sick and mutated them into clones of a genetic undersea creature. The ship was scuttled when the experiment(s) went out of hand.
Despite the bodies being flushed, a piece of Sixpack's mutating leg remains on board and continues to mutate into a lamprey/leech-like creature. This attacks Dejesus in the kitchen. Jones tried to get help, but the creature assimilates Dejesus and begins growing tentacles that randomly attack the crew. Cobb's injuries cause him to mutate as well and he infects Dr. Thompson.
As his last act of free will, Thompson ejects the escape pods so that no one can escape whilst there is a potentially dangerous mutagen on board. Jones, Willie, and Beck are the only ones left and consult with Martin for emergency evacuation. Martin assures them that they won't be left behind, but that she cannot carry out the rescue yet because of the poor weather on the surface.
The crew, suspicious, try accessing weather information through the computer, but it is blocked. Williams is smart enough to not ask the computer for a weather report, but a financial one from the company itself. They discover that the Tri-Oceanic Corp has already declared them dead, labeling it an accident. With the station suffering structural damage because of the creature, they decide to use their special dive suits as a means to escape, leaving the creature behind.
The creature attacks them while they are escaping, but they make it to the surface where they are met by the coast guard. However, the mutant creature surfaces near them and attacks Jones. Jones stalls it at the cost of his life and Beck uses the opportunity to end the creature by throwing an explosive into its mouth.
After they are hauled on-board a ship, the two survivors are greeted by Martin. Martin tells them she believed they would make it, smiling insincerely. Without breaking stride or pausing as he walks past her, Beck punches her in the face, knocking her out, for obvious reasons.