A series of earthquakes affects Quetzo. Dexter returns and takes over Quetzo. Flipper and a lab dolphin named Ultra along with Lopaka drive Dexter out.
New arrivals come to Illoka consisting of Barnacle Crab, Kim and Simon. They are pirates under the guise of filmmakers. Meanwhile, Flipper aided by a reluctant Dexter rescues Ottie.
Bolo stows away on Barnacle's sub but gets trapped. Ultra faces her fear of currents to help Flipper and Lopaka rescue Bolo.
Illoka is holding a talent show and Lopaka finds out that Barnacle and his crew are actually pirates. At the talent show, Lopaka manages to expose them.
Flipper and Lopaka travel to the past, where they return the cursed statue of Neptune to the sea. In another time period they have sink the statue again when Captain Redbeard gets hold of it.
Flipper, Lopaka and their friends carry out a plan to remove Barnacle's ship. Ultra is discovered to be spying for the pirates, but she helps thwart Dexter from sabotaging their plan.
The pirates have returned. While Flipper drives Barnacle and Kim away, Lopaka saves Simon from drowning.
Simon takes Puffy away. Flipper's rescue attempt gets him captured by the pirates. Bolo trying to attack the pirates gets himself captured. Lopaka rescues them and Ultra joins Flipper.
Dexter gets hold of some dynamite from the pirates. Lopaka has no alternative but to reveal his secrets to his people. Together the Milahouni and the dolphins thwart Dexter's plan and dispose of the dynamite.
With Lopaka's secrets out, he can't get any rest. A gigantic shark causes terror, but Flipper is able to get it unwittingly to save Illoka from the unmanned pirate ship.
Lopaka sustains injuries and is marooned with Bermana on a sand bar. Dexter captures Flipper's father. After Flipper rescues Lopaka, Bermana rescues Flipper's father and Dexter's lot.
Captain Barnacle is dumping rubbish in the sea. Sparky, a solitary electric eel encouraged by Flipper helps short circuit the pirate ship.
Fed up with her uncle, Kim leaves, then gets trapped with Nola and Capuna in a ceremonial cave but sends Lopaka and the dolphins to save them. She then rescues Captain Barnacle and Simon who are trapped in a sea abyss.
A sour note from Dexter's organ hurts Flipper. Dexter takes Utra hostage, but the Quetzo fish provide Dexter with a pipe allowing Flipper to sabotage the organ and expel Dexter from Quetzo.
Dexter brings a demonic statue to life which makes all gargoyle statues in Quetzo awaken. The gargoyles turn against Dexter. Flipper and Dexter work together to dispel the magic of the statues.
After a terrible tempest storm Flipper has to rescue Inky, who was captured by vampire fish. Dexter traps Flipper, but Dolores makes Dexter rescue him.
Lopaka and Nola go on the Quest of Courage. Dexter uses a hypnosis charm to get Flipper to do his bidding. Lopaka forfeits the quest and convinces Dexter to help restore Flipper and save Illoka and Quetzo.
Dexter gets injuries, while the Pirates go to Illoka seeking food. Captain Barnacle eats a poisonous fruit, but the Milehouni provide the cure, while Quetzo aids Dexter.
A piece of space junk crashses right into the Quetzo school. Barnacle retrieves the space junk, but his rival Slapbeard takes it and captures Kim and Lopaka, but the dolphins summon the coast guard.
Kim gets a robotic shark but loses the remote to Dexter. Using the roboshark Dexter captures Flipper. The sharks free Flipper to get their jobs back. Lopaka frantically goes after what he thinks is a package of Barnacle's explosives.
Catfish burgalar Lulu La Rue kidnaps Ottie. Ultra rescues Ottie and notices before her capture the statue of Neptune. The only way to rescue Ultra is to get the pirates to winch her out, thus losing the statue to them.
Bolo's bluff about the Milehouni having the trident, gets Barnacle to kidnap Chief Kapuna. The Milehouni create a fake trident for Kapuna's release.
The dolphins and Lopaka go on a long journey, leaving Dexter free to take over Quetzo. While Ottie, Ray and Puffy outwit Dexter, Flipper's lot rescues a fish named Bluey and the pirates from a big fish.
Lopaka manages to put the pirates' radar out of action. Ultra comes across her family and with help from her friends and the pirates drive out a gang of hostile swordfish.
Lopaka, Flipper and Ultra reach the town Seadom, where superstar Dolores has Neptune's trident. Dexter comes, gets the trident and hands it to Barnacle, but Dolores helps recover it.
Dexter steals the trident and hands it the pirates. As the storms grow, Lopaka manages to persuade Kim to give up the statue. After Flipper and Lopaka drop the statue into the black abyss freeing Quetzo and Illoka from the curses.