With the absence of Flipper's parents, Dexter returns with allies to retake Quetzo. Meanwhile, Lopaka and Nola follow Bolo's trail on the dangerous Tabu Island.
Dexter steers Troy to Quetzo, so he can steal Flipper's throne. When that fails, he uses the sun's eclipse to his advantage. With help from Troy's submarine, Flipper gets his throne back.
Dexter decides to do things Troy's way to reverse the Quetzo disaster. Realising Troy's intentions, Lopaka and Flipper seek to be the first to procure the crystals.
Dexter hopes to put Flipper in a bad light during a carnival in Quetzo. He uses Puffy to lure the fish into a trap, but Flipper thwarts the ruse.
While Spike is going on a treasure hunt event, Flipper prompts Dexter to drive Troy away from Quetzo so Franny the manatee can safely give birth, but then Lopaka has to come to Troy's rescue.
Dexter plans to switch the Quetzo crown with a fake one to rig his place as ruler of Quetzo. Lopaka warns Illoka of an incoming tsunami.
Bolo wants to build a flying machine, prompting everyone else to try. Dexter believes he is destined to fly, which Troy takes advantage of to make money.
Troy and Goose brave the Temple of the Four Elements and get one of the crystals. Dexter accidentally swallows the crystal. Only Achuca berries can save his skin.
Illoka fever has affected Chief Kapuna and Lopaka goes with Flipper to acquire the cure from Dexter's grotto. Troy becomes highly interested in the curing plant.
Dexter gets hold of a Quetzo machine from the Tabu cave to invade Flipper's palace. Nola helps Lopaka find the weakness to the machine.
Dexter steals a power crystal, while Troy causes a cave in. Flipper comes to the rescue and recovers the crystal while Lopaka set off to prove Spike did not steal Kapuna's mask.
Dexter steals from Troy an ancient key to unlock a chamber in Quetzo and accidentally triggers a staff to resurrect a dinosaur. Lopaka lures the dinosaur and reverses the summoning.
After a failed attemopt to recover an emerald necklace, Lopaka locates Nola and Spike stranded on an island, and helps inhabitants defeat the Morgue beast.
Troy captures a rare sea dragon and Dexter takes a sea dragon egg. Lopaka rescues the sea dragon and her baby and has Dexter takes their place.
Spike tricks Goose into searching for Captain Cutlass' sunken ship. However their submersible puts Ray and his family in jeopardy. The ghost matter is cleared up and the ship returned to the seabed.
Lopaka and Flipper discover a power crystal that conjures storms. Goose messes with the crystal forcing Lopaka to head there and recover the crystal.
Dexter babysits his niece Inky, but barracudas kidnap her. Flipper and Lopaka assist in the rescue, while Goose and Spike face a giant spider on their day off.
Flipper captured along with Dexter and the sharks by Troy as birthday presents for her friend's son Jeffrey. Flipper convinces Jeffrey to allow him to remain free.
Dexter gets Orci to run a carnival in Quetzo for him, making Flipper feel left out. Flipper saves Orci's mother from Troy's trap and Flipper returns to reclaim his place at the carnival.
Professor Hefty and Jessica come to visit. Dexter unleashes an ancient crab, while Flipper becomes deaf from an explosion. Flipper defeats the crab, while Spike exposes Jessica as a thief.
Dexter gets hold of the fire power crystal and tries to boil up Quetzo, while the ice power crystal freezes Tabu Island. Lopaka gets the ice crystal and unites with the fire crystal.
Dexter recruits a dolphin raised by sharks named Storm to replace Flipper. Lopaka rescues Flipper, who manages to convince Storm, that Dexter used him to conquer Quetzo.
Some holidaymakers come to Illoka, giving the locals a taste of modernisation. Meanwhile, a sea snake rampages due to a tradition neglected, so Lopaka makes a tribute.
Flipper finds the power crystal control panel, then gets hold of a weapon and the final power crystal. Lopaka liberates the weapon and crystal to free Spike and Bolo from a mine.
Dexter takes all seven crystals from Flipper and delivers them to Troy. Unable to talk Troy out of her sacrificial experiment, Spike does instead. Dexter's attempt to finish the job, destroys Tabu.