On Amity Island, sheriff Martin Brody, the hero of previous shark attacks, has died from a heart attack. His wife, Ellen Brody, thinks it was from fear of sharks. She now lives with their son Sean and his fiancée Tiffany. Sean works as a police deputy and is sent to clear a log from a buoy a few days before Christmas. As he does so, a massive great white shark bursts out of the water, rips off his arm, and then pulls him under the surface and kills him, sinking his boat in the process.
Ellen is convinced that the shark targeted Sean on purpose. She decides to go to the Bahamas to spend time with her older son Michael, his wife Carla, and their five-year-old daughter Thea. In the islands, Ellen meets carefree airplane pilot Hoagie. Michael - along with partners Jake, William, and Clarence - works as a marine biologist.
The shark that killed Sean unexpectedly appears and attempts to devour Michael while he's sitting on the edge of their boat. The crew decides to keep quiet about the shark's presence due to Ellen's attempts to convince Michael to find a job on land. Ellen becomes so obsessive that she starts having nightmares of being attacked by a shark. Then she starts getting psychic feelings when the shark attacks Michael. She and the shark seem to share a strange connection that is unexplained.
The crew decides to attach a device to the shark that would track its heartbeat. Using chum to attract it, Jake stabs the device's tracking pole into the beast's side. The next day, Michael is chased by the shark and barely manages to escape unharmed.
Thea goes on an inflatable banana boat with her friend Margaret and her mother. The shark attack and kills Margaret's mother. Ellen is horrified. She goes on Jake's boat, intending to sacrifice herself to stop the killing.
Michael and Jake are flown by Hoagie to look for Ellen and find the shark in pursuit of their boat (which Ellen has hijacked). Hoagie lands the plane on the water, ordering Michael and Jake swim to the boat as the shark drags the plane and Hoagie underwater.
Much to Ellen's disbelief, Hoagie survives. Jake and Michael hastily put together an explosive powered by electrical impulses. They begin blasting the shark with the impulses, which begin to drive it mad; it repeatedly jumps out of the water, screaming in pain. As Jake moves to the front of the boat, the shark lunges, giving it the chance to pull Jake under and maul him. He manages to get the explosive into the shark's mouth before he is dragged under.
Michael continues to blast the shark with the impulses, causing it to leap out of the water again, igniting the bomb as Ellen rams the shark with the sailboat. The broken bowsprit impales the shark, which explodes upon impact. The bow of the ship sinks to the bottom of the sea with the creature's corpse.
Michael then hears Jake, severely injured but alive, floating in the water. The four survive the harsh encounter and make it back to land. Hoagie flies Ellen back to Amity Island.