Martin, CEO of Tri-Oceanic Corp., hires geologist Steven Beck to supervise an undersea mining operation for six months. The crew consists of members Doc, Willie, Sixpack, Jones, DeJesus, Bowman and Cobb. While working outside their deep sea station in a pressure suit, Sixpack discovers a Soviet shipwreck, Leviathan. The crew salvage a safe from Leviathan, finding records detailing the deaths of several crew members as well as a video log from the captain. Sixpack also finds a flask of vodka which he shares with Bowman. Doc and Beck review the captain's video, which describes puzzling medical problems amongst his crew. They also discover that Leviathan was scuttled.
The following morning, Sixpack feels sick and Doc discovers lesions along his back. He dies a few hours later, but Doc and Beck keep it quiet to avoid a panic. Doc checks the crew to confirm no one else is sick, but does not have the chance to examine Bowman. While Beck and Doc confer with Martin on the surface, Bowman begins feeling ill. She finds Sixpack's corpse, which is mutating and growing. When Bowman's hair starts falling out, she realizes the same thing is happening to her. Beck and Doc request emergency evacuation, but Martin reports a severe storm on the surface that will delay evacuation for 12 hours.
Doc finds that Bowman killed herself. Her body is taken to sickbay, where it merges with Sixpack's. When the crew discovers the mutating bodies, they decide to dump both of them in the ocean. As they are about to "flush" the cadavers, the body bag begins squirming. Believing someone inside may be alive, the crew opens it. The creature inside claws Cobb before they eject it. They realize that Leviathan was experimenting on its unwitting crew with mutagens. The mutagen was mixed with the vodka that the crew, and later Sixpack and Bowman, drank. The ship was scuttled when the experiment escaped control.
A tentacle was severed when the corpses were ejected; it mutates into a lamprey-like creature that attacks DeJesus in the kitchen. Jones seals the kitchen's pressure doors and goes for help. He asks Cobb to watch the door, but when he searches for a weapon, the creature assimilates DeJesus and rips its way out of the kitchen. It then grows tentacles that attack the crew.
The creature attacks the medical bay, devouring blood and plasma from the cooler. This inspires Beck to use a pint of his blood to attract the beast, then attempt to flush it the same way they did with Sixpack and Bowman. Doc ejects the escape pods so that no one can escape and risk bringing the mutagen to the surface. Beck consults with Martin for emergency evacuation. Martin assures them that they will not be left behind, but that she cannot carry out the rescue because of a hurricane.
Cobb's injuries worsen, causing him to mutate and infect Doc. Williams escapes as Beck and Jones try trapping the creature. They escape to another part of the station. The crew tries accessing weather information through the computer, but it is blocked. Williams asks the computer for a financial report from the company and they discover that Tri-Oceanic Corporation has declared them dead, labeling it an accident.
The creature damages vital systems, causing the pressure to drop and an implosion to occur. They decide to use their dive suits to escape. The creature attacks them, but is crushed by the lift as Beck escapes. They make it to the surface, which is calm and sunny. As they are met by a Coast Guard helicopter, the mutant surfaces nearby and tries to take Jones. He keeps it from escaping at the cost of his own life, and Beck throws a demolition charge into the creature's mouth, causing it to explode.
After they are dropped off on a Tri-Oceanic oil drilling platform, the two survivors are greeted by Martin. Martin tells them she believed they would make it, smiling insincerely and asking how Beck feels. Beck punches Martin in the face, knocking her out, and then answers her question by saying "Better. A lot better."

Question: What did the crew remove from the Leviathan?
Answer: a safe