Dr. Emma Collins continues the work of her deceased father on the protection of Great White Sharks on an artificial island named Little Happy. Her team includes Spinnaker (nicknamed “Spinn”), Miya and Eugene Shaw, Emma’s father best friend and brother figure. Also living on Little Happy are Nandi and his brother Bahari, others of Emma’s friends. Bella (the bull shark main antagonist from the previous film) is found dead, having been killed after being stuck in fishing lines, discovered by Dr. Richard Lowell and his team on their boat, the Thasos. They go to Little Happy to find the three last pups of Bella are now now adults, and are the only survivors from the litter in the last movie.
Richard is revealed to be Emma’s ex-boyfriend. When Richard and his team dive to chase the bull sharks, Emma dives too and discovers three White Sharks devoured by the bull sharks. Soon after, Brown (a member of Richard’s team) is found dead, having been sliced in half by the bull sharks. With Emma’s help, one of the biggest bull sharks is sedated and captured but Richard is injured.
Later, Bahari goes fishing is attacked and devoured by one of the two remaining bulls. Nandi later discovers his arm. After the loss of her friend, Emma confronts Richard. He reveals her that these bull sharks are more intelligent (explaining the events from the two previous films). He says that with the tag of their mother, he can attire to him as they know that their mother is dead. He concludes in saying that if these sharks reproduce, it will be a catastrophe. Lucas, leader of the mercenaries of Genotic Labs, overthrows Richard’s command and decides to kill everyone and flee with the shark captured. They place a bomb to blow everything up.
During the fight, Emma escapes but Richard is captured by Schill and Earls, Lucas’s men, and brought to the Thasos. Earls is killed by a bull shark while he fought and is defeated by Shaw.
After choosing Emma’s side, Richard is killed by one of two bulls as he jumps to the boat to join her. Emma deactivates the bomb but is attacked by Schill, who has been instructed by Lucas to kill her. She is saved by Sally, the Great White Shark, “friend” of Emma since her arrival on Little Happy, who devours Schill. Emma places the bomb on the Thasos and when Lucas explodes it, his boat sinks and the shark captured is rescued by his brothers. Meanwhile, Spinn is killed by a bull shark and Miya is presumed to suffer the same fate.
Shaw sacrifices himself to kill two of bull sharks with explosive darts. Lucas is revealed to survive at the Thasos’s explosion but is killed by Emma who kills the last bull shark with the garbage compactor.
Nandi and Emma flee, leaving Little Happy sunk, with Sally addressing a goodbye to Emma before disappearing into the ocean. While Nandi and Emma navigate, they found a wardrobe and Miya is revealed alive, having hidden inside it. Reunited, the three friends go back to civilization.