In a remote underwater facility, doctors Susan McCallister and Jim Whitlock (Stellan Skarsgård) are conducting research on Mako sharks with the aim of reactivating dormant brain cells similar to those in Alzheimer's disease patients. The situation takes a turn when one of the sharks manages to escape and sets its sights on a boat carrying a group of young adults. Fortunately, wrangler Carter Blake intervenes just in time, expertly firing darts to subdue the shark and return it to its holding pen. Concerned about the incident and their substantial $200 million investment, the corporate executive Russell Franklin from Chimera Pharmaceuticals is sent to assess the situation at the facility, which was originally a Navy submarine refueling station.
The facility is home to three test sharks: two first-generation and one second-generation female, all monitored by a small crew that has thinned out for the weekend. The facility's engineer, Tom Scoggins (Michael Rapaport), insists that he followed protocol and closed the titanium-laced pens properly, leading to speculation about how the shark could have escaped. Meanwhile, Carter warns Susan that the sharks are displaying unusual behavior, hunting in packs—a sign of their enhanced intelligence due to genetic modifications. Susan, however, threatens Carter, cautioning him against mentioning their research to Russell, as his criminal background would ruin any chance of future employment.
As their research proceeds, Susan and Jim demonstrate the success of their experiments by extracting a complex protein from their largest shark. In a shocking incident, the shark bites off Jim's arm as it is being examined. In a moment of desperation, Susan releases the shark before Carter can eliminate it. Chaos ensues when operator Brenda Kerns (Aida Turturro) calls for a helicopter to evacuate Jim, but the lift goes horribly wrong, causing a series of catastrophic explosions that ravage the facility.
With the facility flooding rapidly, Susan confesses to the others about the genetically engineered sharks, revealing that in their attempts to boost their brain size, they have inadvertently created smarter and more dangerous predators. As they scramble to find an escape route, Russell’s motivational monologue about teamwork is cut short when a shark drags him into the depths and devours him. The remaining crew decides to ascend the flooded elevator shaft, but tragedy strikes again when Janice Higgins (Jacqueline McKenzie) falls victim to one of the sharks.
In the kitchen where water is rising perilously, cook Sherman "Preacher" Dudley (LL Cool J) bravely manages to kill the first shark using an explosive trap. He then joins Carter, Tom, and Susan, who are racing against time to reach a control panel necessary for draining water from the facility. However, another shark storms in, killing Tom and sabotaging their escape route. In a desperate bid for survival, Susan faces yet another shark and manages to electrocute it, but this leads to the loss of her crucial research.
Finally regrouping, Carter, Susan, and Preacher make their way to a decompression chamber to escape the flooding facility. Preacher is viciously grabbed by the remaining shark, yet he fights back and escapes with serious injuries. Only one test shark is left now. Understanding the sharks' strategy, Carter readies a harpoon armed with explosives, while Susan selflessly distracts the shark by diving into the water, ultimately sacrificing herself in the process.
As Carter clings to the dorsal fin of the shark, Preacher follows through with the harpoon, inadvertently injuring Carter. In a final stand, they manage to critically wound the shark as it attempts to flee through the weakened barrier. With courage and tenacity, Carter and Preacher make it to the surface, where they catch sight of a rescue boat on the horizon, hopeful for survival.
