Flipper is abducted by Keith Ricks' old fraternity brother to serve as the chief entertainment at a new Cuban resort hotel. Ricks and Pam Blondell attempt to sneak into the Caribbean country to rescue the dolphin, but are captured and imprisoned by the Cuban Coast Guard.
Flipper refuses to perform for the grand opening of a Cuban hotel resort. With the help of a beautiful local woman, Ricks breaks out of jail and plots to rescue the dolphin before the vengeful resort owner can kill the reluctant dolphin.
Mike and Maya take the Institute's new submersible out to sea to try to photograph the mermaid the two youngsters think they saw. Mike's inexperience places them in deadly peril when they get trapped hundreds of feet below the ocean surface.
Allison Van Rijn, a beautiful underwater photographer with a pet moray eel, moves to Bal Harbor and corpses begin to accumulate immediately thereafter. Keith and Flipper don't trust the newcomer, but Pam stands up for Allison.
Flipper discovers some strange equipment on the floor of the ocean and convinces Keith and Pam to follow him to the location. The two scientists are mystified by the set-up; the more so when two thugs tie them up and dump them overboard far offshore. With the help of Flipper, they escape and discover a plot to produce genetically altered pearl oysters that are capable of reproducing at an astounding rate and threatening Florida's coral reefs.
Keith and Pamela elect to remain at the institute with Aphrodite, a dolphin in the final stages of a difficult pregnancy, as a Category 4 hurricane bears down on their island.
While Keith and Pam try to convince a wealthy older woman to contribute to the Institute, Mike and Maya get involved in the local surfing scene and are soon mixed up with a gang of hip young hoodlums.
The lives of the Institute's staff are turned upside down when benefactor Sydney Brewster moves in and attempts to reorganize its operations. Meanwhile Maya moves in with Pam and Mike while her sister looks for work out of state.
Flipper shepherds a sick dolphin to the Institute and the team members discover that animal's illness has been caused by contact with a toxic substance. While Keith and Pam desperately seek to locate the pollution's source, more and more dolphins wash up on the beach with the same symptoms.
Bobby Grimes, the brother of a Carl Grimes, a man Keith Ricks sent to prison and who subsequently died while incarcerated, turns up in Bal Harbor to menace Keith, Pam and their young charges. Not content with avenging himself upon Dr. Ricks, the sociopath is determined to kill all his friends first.
When sharks attack swimmers off a Florida island slated for a new resort hotel, Keith investigates and discovers that endangered fish species have been introduced to the area by a rival hotel owner.
