Dr. Pam Blondel, a U.S. Navy officer, is hired to join Dr. Ricks' dolphin research team, but her son isn't happy to be living in remote Bal Harbor.

An attack by pirates starts a headlong treasure hunt.

A tuna fisherman is framed for cruelly battering dolphins by an unfaithful wife and her scheming boyfriend.

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.

Keith Ricks' brother Sandy helps the Institute's staff battle shark poachers.

Mike tries to bring his divorced parents back together with the help of Maya's magic charm.

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.

Pam tries to help an amnesiac plane-crash victim using Flipper and Aphrodite for dolphin therapy.

International criminals force Keith and Garcia to help them locate a Cuban nuclear missile submerged in Florida coastal waters.

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.

Mike is infected with a deadly virus when he accidentally visits a small island populated by diseased monkeys.

Flipper is accused of attacking two humans and Dr. Ricks' satellite tracking device confirms that the dolphin was in the area.

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.

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.

Keith suffers nightmarish delusions from nitrogen narcosis he sustained because of a diving accident.