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There is no Next Episode of Flipper & Lopaka planned.
Flipper introduces Lopaka to his underwater home - the legendary lost city of Quetzo. When Dexter hears that a human is in the city, he claims it breaks an 'unwritten law' and puts Flipper and Lopaka on trial before all the citizens of Quetzo.
An old carved stone is unearthed on Iloka. Its inscription states that when the stone is returned to its temple, the Milihune will return to Quetzo. Chief Kapuna becomes convinced that the stone is bad luck and throws it into the sea. Dexter finds it and, determined not to let the Milihune get into Quetzo, keeps the stone. Flipper and Lopaka, however, want to return it to the temple.
Iloka's dormant volcano, Old Grumbly, is beginning to show signs of activity. Kerava assures the villagers it cannot erupt, because the main vent was blocked years ago by an ancestor of Lopaka. However, Dexter intends to remove the blockage so that Old Grumbly will erupt and get rid of the Milihune.
Professor Ahab, a marine biologist, anchors off Iloka to capture a white whale for research. Underwater, Flipper is learning to use his innate sense of direction when he is disorientated by the sonar from Ahab's boat. Flipper and Lopaka escape the sonar by swimming to Flipper's Grotto, where they discover a white whale and her baby hiding.
It's Nola's birthday, so Lopaka sets off in search of a valuable gift. But thanLopaka has a decision to make: Does he want to walk off with fame for the most beautiful birthday present for his friend Nola or save an impoverished fish family from ruin?
A killer whale - Orkie - returns to Quetzo to settle an old feud with Flipper. Dexter, determined to provoke a big showdown between the two, gets Orkie really angry and then convinces the rest of the town not to help Flipper. Finally Flipper and Orkie and they end their feud to save the school.
While defending Quetzo against a gang of predatory sharks, Flipper and Lopaka get unexpected help from a renegade shark. With their new ally, Flipper and Lopaka race towards Iloka where they chase off the other sawtooths, who are threatening the villagers competing in a diving contest.
Dexter and his henchmen have a big feast, but make a mess of Quetzo with their litter. Flipper makes them clean it up, but the sharks secretly dump it in the Big Deep. The next day Iloka is terrorized by a huge sea serpent. Lopaka and Flipper discover that the serpent is from the Big Deep, and has some of Dexter's rubbish caught in its throat.
A drought on Iloka starts a desperate search for water. Flipper, in an attempt to solve Iloka's water shortage, tricks Dexter into finding an iceberg, then bringing it back to Iloka.The iceberg melts and the water pours into Bomana's well, filling the legendary underground stream.
Vain villain Dexter is trying to get the main part in a monster movie by any means.However, the director thinks Dexter looks too mechanical and 'unrealistic' and won't use him. Offended, Dexter decides to make the movie himself and kidnaps the director and his camera.
Chief Kapuna's leadership is threatened when Dexter steals his crown, which should glow as a sign, that he is the rightful chief. So when the fake crown fails to glow, the villagers doubt Chief Kapuna's leadership. However, Flipper and Lopaka realize there has been a switch and swap the crowns back, just as Dexter is about to crown himself King of Quetzo.
Chief Kapuna believes his long lost brother, Bunti, has returned to Iloka. A decade earlier, Bunti had gone missing at sea just after being crowned chief. Kapuna was crowned in Bunti's place, and so he is uneasy about his return. But nobody on the island has actually seen Bunti - only heard him whistle. So Flipper begins to investigate.
Jojo, a little blue fish, who is held up to his brothers' ridicule every day, is unexpectedly given the chance to assert himself, when he helps Flipper and Lopaka to save Dexter, who is buried alive in a submarine cave. So Jojo finally has confidence in himself, and a new-found respect from his brothers.
An oil spill has contaminated the water around the island of Iloka and is polluting the food supply. This gives Dexter the idea to use the oil to drive the Milihune off the island. But Flipper, Lopaka and Charlie the Dugong trie to prevent Dexters Plan and save the Milihunes.
Lopaka and his friends put on a circus for the village. Dexter, who is watching off-shore, decides to put on a similar show underwater, as a money-making scheme. After the show, Dexter steals the circus equipment and takes it to Quetzo. Bolo accuses Lopaka of dumping the equipment, prompting Lopaka and Flipper to search for it.
A family of stonefish arrives in Quetzo and is shunned by the locals, who are afraid of their grotesque appearance and poisonous spikes. Dexter carelessly pricks himself on one of the fish, and reveals he has the only known cure for their poison. So when Nola accidentally treads on one of the stonefish, Lopaka begs Dexter for the antidote.
Dexter steals a book from Calabash and discovers it contains instructions for building a powerful cannon. He and his henchmen manage to gather all the components for the weapon, except the firing pin. They discover this is being used as the medal for Quetzo's Aqua-olympics tennis competition. So Dexter enters the contest and steals the pin.
Dexter decides to improve his financial status by becoming mayor of Quetzo. When Flipper points out that a by-law insists the mayor must be married, Isolde, a jellyfish, disguises herself as a beautiful octopus, to trick him into marrying her. Flipper and Lopaka find out and stop the wedding at the last minute.
Iloka is threatened by a king tide, so the islanders build a wall around their village to keep the water out. However, Dexter breaches the wall and, as the sea rushes in, the villagers are forced to flee up the mountain. With the village underwater, Dexter and his henchmen move in and seal the wall behind them, proclaiming Dexter King of Iloka.
Dexter takes a group of mischievous young fish under his 'wing.' Concerned at the influence these delinquents might have on other youngsters, Flipper forms a sporting team to promote positive values.The delinquents are so impressed that Flipper's team managed to win without cheating, they switch sides.
Dexter's niece Inky has joined Flipper's youth group. Shocked that his niece is friends with Flipper, Dexter decides to teach Inky a lesson by trapping her and her friends in an old ship. However, Dexter and the sharks get caught instead, and Flipper and Inky save them.
Bolo keeps getting into trouble because of his silly behavior, so he decides to run away. When Lopaka catches Bolo sneaking off, Bolo makes him promise not to tell anyone where he's going. But Bolo is captured by Dexter's sharks and dragged out into the current. With Flipper's help, Lopaka manages to save Bolo, who thanks Lopaka for not keeping his promise after all.
Nola, who is out surfing secretly, sees a giant water spout approaching the village and surfs back to warn them. Thanks to Nola, the villagers are saved - only Dexter and his surfboard get caught in the water spout!
Dexter wants to show that he's a hero by rescuing Lopaka - but first he has to trap him! When Flipper finds out about the plan, he races to the island to warn Lopaka, but gets beached on the shore during a storm. Fortunately, Bolo finds Flipper and puts him back in the sea. Meanwhile lopaka gets trapped by Dexter.
Dexter finds an old human diving suit and fills it with water, so he can walk on land and invade Iloka. To prevent Flipper from interfering, Dexter traps him in an underwater cave. The islanders try to fight off Dexter as he stomps around the island, but eventually flee in their canoes. Lopaka, Nola and Bolo remain on the island and defeat Dexter.
Dexter discovers the missing crown of Quetzo and is about to enthrone himself as king, when the real sovereigns of Quetzo appear - Flipper's parents, the real King and Queen of Quetzo! Dexter is then banished to the Big Deep, Flipper becomes Prince of Quetzo and Lopaka returns to Iloka to become the new wise man of the village.