Banished from the village by Chief Pondo, Korg wants to get even so he sends an army of animals to attack. He then demands that Pondo step down and appoint him the new chief or he will bring his animals back and destroy the village. Tor, not wanting his friends to be harmed, turns into Mightor and does battle with Korg.
An underwater earthquake buries Moby and the boys under tons of rock. But they end up in an undersea world where Moby Dick has to protect Scooby and the boys from various dangerous creatures like giant insects, clams, mutant seaweed, eels, and Reptile Men as they try to find their way home.
Li'l Rok is trapped on a ledge by a giant dinosaur. Tor slips away, turns into Mightor and heads off to try and save his friend. He throws the dinosaur into the swamp only to discover that Li'l Rok has disappeared. Searching, Mightor find a nearby village where the residents have been enslaved by a group of humanoid insect creatures.
Grok orders Tyrannor, a giant T-Rex, to throw a boulder at the village. He then challenges the village to produce Mightor to fight Tyrannor or he will destroy the village.
While exploring an old sunken ship, the boys and Scooby encounter Crab Creatures that capture Tubb. Tom and Scooby go to find Moby so he can try to rescue their friend.
Brutor the Barbarian is leading his army of creatures in an attack on the village when they come across Tog and bring him down with one of their weapons. Tor tells Sheera and Li'l Rok to warn Chief Pondo and the villagers of Brutor's plan.
Sheera is captured by the Bird People while getting water at the river. When she doesn't return to the village, Tor goes in search of her. He turns himself into Mightor and discovers her by the lava pits where she is about to be sacrificed to their god Dogar.
Tom and Tub are surfing on waves created by Moby jumping in the ocean when they smash into an iceberg that had drifted down from the North. When they go down for a look under the surface they discover something frozen within the ice. A piece of the iceberg breaks off releasing the creature who tries to attack Scooby and the boys.
Sheera is captured by the Cavern Creatures who take her to Kragor. Bollo returns to the village without Sheera and Li'l Rok so Tor knows something is wrong. He discovers that the entrance to the where the Cavern Creatures and Kragor live is open and realizes that they must be to blame for his friends disappearance.
The Tiger Men decide to attack the cave people as their god demands a sacrifice. The Tiger Men capture Tor and to punish him for alerting the others, take him to the arena. Tog needs to get Tor's club before the saber-toothed tiger does him in at the arena.
Tom and Tubb see three Saucer Shells approaching and know that it means trouble. The boys see them go after a group of dolphins and decide to help. The Saucer Shells go after the boys who retreat towards Moby Dick for some help of their own. Scooby gets captured and now it's up to the boys and Moby to rescue him.
While the men are off hunting a giant ape appears and captures Sheera. Mighty Mightor returns quickly, discovers what has happened, he goes after Sheera. He finds that the ape yook her to his nemesis, Korg.
Sheera's mammoth cub, Bollo, disappears and she sets out to find him, unaware that the Tusk People have kidnapped him. Tor and Tog realize that Sheera and Bollo are missing and notice their footprints mixed in with those of the Tusk People. Tor turns himself into Mightor in an effort to save them both.
Tom and Tubb are swimming in the ocean when a pair of tiger sharks begin chasing them. Scooby races to find Moby Dick so that he can help the boys. As Moby chases the tiger sharks away, Tubb inadvertently swims inside the mouth of a giant fish. Tom rushes off to find Moby in an effort to save Tubb.
Sheera and Tor hear thunder during a snowstorm and discuss how it's said to be the voices of the Snow Trappers. Li'l Rok doesn't believe the stories and decides to take Ork with him on a search for the fabled monsters when he's captured by one. Ork returns to get help and Sheera sets out to save her brother only to be captured herself.
Sheera is kidnapped by one of the Serpent Queen's underlings to be turned into her slave. When Pondo and Tor discover Sheera missing, Tor heads off for help. When he is out of sight he turns into Mightor and returns to Pondo to offer his assistance.
Underwater bat creatures attack Moby, Scooby and the boys. Tom and Tubb are taken prisoner by the Aqua-Bats who are eventually frightened off by giant Portuguese Man-0-War.
The Giant Hunters, an evil group of creatures, come upon Chief Pondo's village and capture Tor and Tog. Fortunately, Tor has his club and is able to turn himself into Mightor and the battle is on.
Tor is teaching Li'l Rok that to survive in the jungle, you must always be alert. They hear a signal call of the Tree Pygmies and prepare to run when Tor is captured and loses his club. Without it, he will not be able to turn into Mightor. Li'l Rok returns to the village to get help from Ork and Tog.
Tom and Tubb have been captured by the evil Shark Men with Moby and Scooby in pursuit. The Shark Men trap Moby in a cave. Moby manages to escape from the cave and now must set out in an effort to save the two boys.
Tor, Sheera, Li'l Rok and their pets get trapped in a cave during a storm. Looking for another way out, they find themselves in the Valley of the Volcanoes where Charr and the Fire People live. The Fire People see the intruders and begin an attack. Tor finds himself trapped in a deep pit while the others are captured.
The Stone Men enter the village in their giant stone dragon looking for slaves and capture Sheera. When Tor sees that Sheera is captured, he offers himself as a slave in exchange for her release. The Stone Men go back on their word and keep them both as slaves. Tor is now without his club and must find some way to get it if he is to save them both.
Tom, Tubb and Scooby are water skiing behind their friend Moby when they notice what looks like a space capsule about to splash down in the ocean. Manta Menace is waiting for the capsule and its contents: the secret maps of the Mars diamond mines. The boys see the capsule sink and have Moby take them in so they can investigate.
Li'l Rok is off by himself exploring when he comes across the Forbidden Temple of the Scorpion and is captured by the Scorpion Men. Sheera and Tor start to search for him when he hasn't returned by dark. Sheera is captured next, but Tor hears Bollo's call and turns himself into Mightor so he can attempt a rescue.
Tor is kidnapped by the Gill Men who bring him to the Serpent Queen. She wants to use him as bait to get revenge on Mightor. Li'l Rok, who witnessed the kidnapping, takes Tor's club and flies off with Ork to deliver it to Tor so he can battle the Queen's Serpent of the Pool.
Moby is caught by a giant squid and the two get into a fight to the finish. Moraya witnesses the fight and wants to use him to test her trained fighters. She orders her men to capture Tubb and Tom to use as bait to lure Moby in to where he can be captured himself. Moby is indeed captured and he and the boys must fight to escape.
Sheera and Li'l Rok get into a race with Tor while traveling on their rafts down a river. Tor gets caught up on some rocks and loses sight of his friends who find themselves shooting through rapids and landing on Vampire Island. Tor realizes that his friends are lost and turns himself into Mightor to attempt a rescue.
The Vulture Men have created a Great Stone Vulture in which they plan to entomb Mightor so it will gain his great powers. The villagers see the Vulture Men coming and Tor turns into Mightor to fight them off. They capture Li'l Rok and demand that Mightor surrender. Mightor agrees and is sealed in the Great Stone Vulture.
Tom has Moby take him Tubb and Scooby to an old pirate ship that he discovered on the ocean floor. The boys go inside the ship and find a secret compartment in the Captain's quarters with a treasure map inside. They hear a noise and see the Electrifying Shoctopus: an octopus-shaped underwater craft piloted by Captain Squid. Captain Squid captures the boys and takes their newly found treasure map.
The Ice Creatures plan to move their glacier into the lowlands and take over the village and make Mightor their slave. They have a group of wooly mammoths push the glacier and ride it down the mountain and into the village. The villagers see the glacier approaching so Tor moves into action and turns himself into Mightor and the battle is on.
The Witchmen set out to find a queen for their ruler. They head to the village and find Sheera and Tor building a fire. They burn a bowl of "leaves of sleep" which incapacitates them both and they kidnap Sheera. Tor deducts that the Witchmen took her so he turns into Mightor and heads off in a rescue attempt.
Tom, Tubb Scooby and Moby witness the evil Cereb Men attacking a city. Upon investigation they discover that the King's son, Prince Zor, prisoner. They demand complete surrender of the city in return for the prince. Can the four friends save Prince Zor and the underwater city?
Chief Pondo and all of the men (except for Tor) go on a hunting trip. While they are away, the Cavebear Warriors come to the village and capture Sheera and Li'l Rok. Tor sees their tracks and turns himself into Mightor so he can attempt a rescue.
Li'l Rok and a group of his friends decide to go rafting down a river to the Black Gorge. Sheera and Tor see the kids and know that it's too dangerous. Sheera takes off after the kids in a canoe while Tor turns himself into Mightor and heads out on a rescue mission. They run into one dangerous situation after another.
Moby and the boys are passing through an unexplored area known as the graveyard of ships. This area is controlled by a group of amphibious creatures led by Toadus and he does not like visitors. The boys begin exploring an old ship and are captured by the creatures.
Tor and Sheera warn Li'l Rok of an approaching Terrible Beaked Bird. Li'l Rok discovers the nest of the creature and decides to retrieve the egg so he will be famous in his village. Sheera and Tor see him in the nest and know he will need help.
Numo and his Sea Slavers capture the women from the village as they are repairing the village fishing nets. The men discover that the women are missing and see the tracks left by Numo and his men. Tor takes quick action and turns himself into Mightor in an effort to follow the ships and rescue the women.
Vortan and his men use a powerful vortex to capture approaching underwater vessels. They turn it on when they pick Moby up on their radar thinking that he is a vessel. Moby and the boys survive the vortex but find themselves trapped between the vortex and Vortan and must fight their way out if they are going to survive.
The Storm King summons extra power from a lightning storm and now claims to have powers greater than Mightor. He appears at the village demanding to see Mightor. Pondo tells him that Mightor is not there and asks him to leave the village in peace. When the Storm King responds by putting Pondo in a deep sleep, Tor uses this distraction to turn into Mightor.
Li'l Rok, Sheera, and Tina are trying to catch butterflies and chase one into a nearby cave. When they come out the other side, they discover a strange world of man-eating plants. Luckily, Tor was following them in case they needed help, however, he loses his club and is captured with the others.
Soodak the Invader arrives on Earth to scout for his invasion forces. He has his men launch their probe units to secure the area. Moby, Scooby and the boys come across some of the probes and Soodak orders them to be captured. Moby destroys the probes but Tom and Tubb are captured by another set of probes.
The Vulture Men are headed for the village to get revenge on Mightor. They arrive and begin dropping boulders from their pterodactyls. Tor turns himself into Mightor and begins chasing them away which is exactly what the Vulture Men wanted. They had sent the winged monsters as decoys so they could attack the village when Mightor left.
Li'l Rok and Ork find themselves lost in Hidden Valley. When Rok is seen by the villagers he's mistaken for their Great Horned god. As their proclaimed "true Champion," Li'l Rok accepts the offer to become their leader and defend the village against the Great White Terror, a creature who's more than Rok can handle.
Tom doesn't believe that Tubb has seen a Mermaid until he sees a Black Manta Knight chase her down and capture her. Moby and the boys follow them into a mysterious Shimmering Screen where they discover another undersea world. They quickly move into action to try and rescue the helpless Mermaid.
Li'l Rok and Ork are fishing when they run into a boy named Norg of the Hill People. Norg is from a neighboring village and is looking for Mightor because Kragor and his Cavern Creatures have attacked his village. Li'l Rok tells Norg that he is Mightor and the two set off to run Kragor out of his village. Tor overhears, turns himself into Mightor, and is off to do battle with Kragor again.
Li'l Rok and Ork are trying to become the first from the village to capture a dinosaur from Dinosaur Island. He's able to snare one in a trap ,but the dinosaur proves to be too strong and makes an easy escape. Sheera and Tor find a note from Li'l Rok explaining where he has gone. Tor turns into Mightor and heads off to Dinosaur Island to help.
Tubb is trying to ride a Sea Pony. After Tubb is thrown off, a pair of Gill Men captures the Sea Pony. Moby and the boys try to free him but Moby is trapped in a cave by a powerful force field and Tom is captured himself. Will Moby be able to get free and help his friends?
The Mountain Monster Tribe's chief has decided that it is time he names his replacement. Gorg and Brog both make claims on the position so the chief proposes a challenge. Whichever of them is able to defeat Mightor will be the next chief.
Li'l Rok and Ork get lost during a storm and are captured by a group of strange insect men. Li'l Rok manages to escape by starting a fire as a distraction. Tor sees the smoke, realizes that Li'l Rok might be in trouble, and turns into Mightor to investigate.
Iguanis of the Iguana Men orders two of his men to capture Tom and Tubb. They are very aware that Moby is their guardian and set a trap to capture them. Scooby alerts Moby that the boys have been captured so he chases after the Iguana Men to try to save his friends.
Grok steals the Golden Rok which has the ability to control any animal. It falls out of his pouch as he is leaving and hits Li'l Rok on the head. While fighting a dinosaur, Li'l Rok discovers the power of the Golden Rok. As he is experimenting with it, Grok returns and steals it back. Tor hears animals fighting in the area that Li'l Rok had headed; he turns himself into Mightor and heads off to investigate.
Tor and Li'l Rok fly to the village of the Valley People to surprise Sheera and discover the village is deserted. They begin investigating and Tor suddenly disappears, leaving his club behind. They discover that Rogg and the Stone Men have kidnapped their friends and plans to use them as slaves to build a stone Dinosaur of War.
Crockor is busy storing power in his laboratory so he can create his Sand Creatures--enough of them to control the entire ocean. Crockor picks up Moby and the boys on his radar and wants to capture them so they don't ruin his plans. They must do battle with Crockor and his Sand Creatures or the ocean may forever be in the hands of the evil genius.
Mightor appears before Chief Pondo and the villagers demanding what is owed to him for all his good deeds. Mightor announces that he plans to become chief of all the villages and that the people will be his slaves. He then commands the warriors to capture Chief Pondo. Sheera and Li'l Rok set off to free their father and run into Tor. They explain what has happened, which makes no sense to Tor since he is the REAL Mightor.