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At a U.S. Navy research base near California's Salton Sea, a four-hundred square mile body of salt water in the middle of an arid desert, top-secret atomic experiments are conducted. A parachute testing unit is also based there and flies daily missions over the sea. Shortly after an earthquake centered below the Salton Sea occurs, two seamen, on a regular mission, wait in a launch to pick up a parachutist when he lands in the water. On this occasion, when they reach the parachute they find no trace of the man. One seaman dives into the water to search for the jumper but does not resurface. The other seaman reacts in horror to the sudden appearance of a giant creature. When the seamen fail to respond to radio messages, naval intelligence officer John "Twill" Twillinger, recently assigned to the base, is alerted and sets out with Lt. Bob "Clem" Clemens to investigate. They find only the body of the one seaman on board and a strange mucus-like substance smeared over the boat. Suddenly, the mangled body of the parachutist floats to the surface. Twill orders an autopsy of both bodies and takes a sample of the substance to Dr. Jess Rogers at the base's laboratory. While waiting for Rogers' evaluation, Twill meets Rogers' secretary, Gail MacKenzie, and her young daughter Sandy. The next day, at the county morgue, the coroner tells Twill and Sheriff Josh Peters that both bodies had been drained of blood and water and that the seaman probably died of a fear-induced stroke. Twill then asks Peters to post a complete ban on swimming in the sea. However, that night, a young couple, unaware of the ban, go swimming and are subsequently reported missing. Twill sends two divers, Tad Johns and George Blake from Rogers' lab, to swim to the bottom of the sea and take radioactivity readings. All appears normal until the divers descend into a cave underneath the sea bottom and find a large, egg-like object that is radioactive. The egg is hauled up to the launch and as Johns and Blake prepare to join it, Blake is captured by a creature and killed. On board the launch, Johns is recounting what happened below when the creature rears up out of the water and threatens them. After Twill drives it away by destroying one of its eyes with a pole, they return to the base where the egg is placed in a controlled temperature water tank. While Rogers consoles Blake's widow, Gail tells Twill that she, too, is a widow, having lost her pilot husband two years earlier. Within a few hours, Twill mounts an expedition to destroy all the creatures and their eggs using underwater explosives. Meanwhile, Rogers explains to military officials his belief that the creatures are descendents of the historically documented Kraken family of water mollusks. Rogers also states that the earthquake probably caused a fissure in the sea's floor through which radioactive water seeped, fertilizing the eggs and causing the creatures to become enormous. Although the cave will be sealed, Rogers fears that some of the creatures could escape into the nearby All-American Canal and threaten the entire world. Although an around-the-clock patrol of the canal system is ordered, two more people are killed. The next day, at a local museum, Twill and Peters attempt to find old maps of underground rivers in the area, but are unsuccessful. After a creature strikes again, killing a gatekeeper at one of the canal's locks, all the locks are closed in an attempt to isolate and trap it. Soon after, Gail's young daughter Sandy enters the lab to see some caged rabbits and, thinking that she is turning up the heat for them, changes the temperature in the water tank. Later, after the museum archivist comes to the command post to deliver an old map of Indian wells, Twill and Rogers survey the mapped area from a helicopter and spot a scum-covered body of water, which they think may contain the creatures. Twill joins Johns on a dive and they locate several dormant creatures, set explosive charges and destroy them. Meanwhile, the egg in the laboratory has hatched, producing a full-size creature, which threatens Gail and Sandy, forcing them to hide in a closet. The creature has almost broken through the closet door when Twill and Rogers return. While Rogers goes for help, Twill diverts the creature's attention by spraying it with the contents of a fire extinguisher, allowing Gail and Sandy to escape. Twill then contains the creature with a hose of hot steam until three riflemen arrive and kill it. Later, Twill, Gail and Sandy walk off together.