Deep in the Democratic Republic of the Congo, an illegal diamond mining operation awakens a giant 1,1000 foot (460 m) prehistoric crocodile. Meanwhile, on the Atlantic Ocean, the US Navy warship USS Gibson is attacked and sunk by the megalodon that ended up surviving suffocation by the octopus in the first film. Lt. Terry McCormick (Jaleel White) who was experimenting with a sonic shark-repelling device, is the sole survivor of the attack.
Back in DR Congo, an English hunter named Nigel Putnam (Gary Stretch) successfully captures the giant crocodile when it attempts to eat him and he injects his tranquilizer darts into its mouth. He then has the crocodile delivered to a shipping yard for his friends to load it in a cargo ship.
In Los Angeles, California, McCormick is being interrogated by the National Oceanic and Atmospheric Administration Special Agent Hutchinson (Sarah Lieving) for the USS Gibson incident. He feels responsible for the sinking, suggesting that his sonic device lured in the megalodon. Because of this, he offers to help Hutchinson hunt down the megalodon with his invention. Meanwhile, a cargo ship is carrying the tranquilized crocodile on the Atlantic Ocean 400 miles south of Florida. It is revealed that the ship is also carrying the crocodile’s eggs as well. Then, without warning, the ship is attacked by the megalodon, waking up the crocodile from its sleep. Putnam and his partner Jean jump overboard before the ship is destroyed in the ensuing battle.
Aboard the aircraft carrier USS Lexington, McCormick is introduced to Admiral Calvin (Robert Picardo), who informs him that his elite crew has only one objective: to hunt down and destroy the megalodon. McCormick is given a room aboard the carrier, and the most advanced tracking equipment. Hutchinson is sent to a remote island to meet and interrogate Putnam, who had just washed up ashore following the cargo ship incident. Hutchinson is shocked when Putnam informs her of the crocodile he captured, as her team was only aware of the megalodon. She then has him handcuffed and brought back to the carrier. Once there, the crew discover the appearance of eggs on another island. Adm. Calvin assigns McCormick to accompany Hutchinson and Putnam and capture an egg. Upon arriving on the island, they discover that the eggs are laid by the shoreline and are about to hatch. When the fin of the megalodon is seen nearby, Hutchinson orders the Lexington to launch a missile strike on the island. As the team leaves the island, the megalodon swallows the eggs, angering the crocodile, while a squadron of F-18 Hornets fire their missiles at a cave holding more eggs. As the crocodile invades Miami and heads toward Orlando, McCormick suggests the use of an arc flash powered by the nearby Turkey Point Nuclear Generating Station to ward it off. The gamble works, as the arc flash sends the crocodile back into the sea.