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.
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 Emma Phelps overhears her husband plotting to maim their prize thoroughbred to get insurance money to pay off a debt, she enlists Cap, Jennifer and Maya's help to hide the horse until the big race the following weekend.
Attendees at the annual Bal Harbor Art Auction are held up by modern day pirates who make their getaway on a pirate ship equipped with a powerful engine. When the pirates learn that Holly Myers, one of Jennifer's students, is the daughter of the auction's millionaire benefactor, they return to the scene of the crime to kidnap the beautiful blonde.