With their home planet, Thundera, about to explode, the Thunderians flee to a distant galaxy. Before they can make the long journey the Mutants sweep in and destroy most of the fleet in an attempt to capture the Eye of Thundera. Due to the attack, the Thundercats find themselves on a distant planet. A grown-up Lion-O must save his Thundercats from the Mutants on Third Earth.

The Mutants, who have also reached Third Earth, encounter an old pyramid. It turns out to be the home of Mumm-Ra the Ever-Living, and they join forces to capture the Sword of Omens. Both the Mutants and Mumm-Ra attempt to attack Lion-O to possess the Sword, but miserably fail.

The Ro-Bear Berbils are a friendly group of robot bears that live on Third Earth. Lion-O and Snarf don't know this, and end up getting caught in a Ro-Bear trap. The Berbils free them however, and they form an alliance. Mumm-ra attacks the Berbil village, but the Thundercats save it. In return, the Ro-Bears help the Thundercats to build Cats' Lair, a new base for the Thundercats.

The homeless Mutants also make plans to build their home. They enslave a primitive race of beings called Brute-Men to do their work for them. The Thundercats go to Castle Plunn-Darr to free the Brute-Men from the Mutants.

Mumm-Ra uses his shapeshifting abilities to pass himself off as a Thunderian so he can stage the "rescue" of Cheetara and infiltrate Cats' Lair.

When Snarf and a young unicorn are captured by the pirate Hammerhand and his crew of Berserkers, Lion-O goes to rescue them.

With their supply of Thundrillium running low, the Thundercats set off in search of a fresh supply. Tygra detects a large deposit in a cave and goes to investigate - unfortunately, he has entered the Cave of Time and anyone who ventures in there will age rapidly until they die. His only hope is that Cheetara's speed will be fast enough to allow her to escape the Cave's effects.

Wilykit and Wilykat try to stop a band of living gargoyles from robbing a Wollo but fail to do so and trail the gargoyles to a nearby Tower. Wilykat is trying force the door open when he suddenly disappears, leaving Wilykit - who was looking for another way in - close to panic. She and Lion-O (alerted by the Sword of Omens) must now brave the Tower's potentially lethal traps in order to rescue Wilykat.

While investigating an earthquake, Tygra stumbles across the Garden of Delights and meets a talking plant named Silky, who offers him her fruit. But it turns out that "Silky" is another of Mumm-Ra's disguises and eating the fruit seems to have affected Tygra's mind.

Lion-O and Snarf stumble upon a portable jail cell, and mistakenly open it up. Three of the galaxy's worst villains escape. One of them, a slick thief, manages to steal Lion-O's sword. Lion-O helps Mandora, the inter-stellar police officer that imprisoned the villains, recapture them, and return them to their cells.

Two Bolkins (sheep-like beings from Third Earth) unleash the ghost of Grune the Destroyer, a renegade Thundercat who once terrorised Third Earth and now turns his attention to the Thundercats.

Mumm-Ra and the Mutants plot to open the Time Warp Prison and release the evil Princess Ta-She in order to use her deadly Doomgaze against the Thundercats.

When a meteorite made of pure Thundrillium crashes on Hook Mountain, the Thundercats decide to use it to replenish their depleted energy supply. But Lion-O must first gain the trust of the fierce Snowman.

Tired of constantly being bested by the Thundercats, the Mutants have Mumm-Ra raise their spaceship and salvage their vehicles.

Lion-O becomes homesick, and his memories of Thundera are almost nonexistent. Jaga appears to Lion-O and tells him that on their spaceship, they brought with them a time capsule which contained a recording of Thundera and its history up to the time it was destroyed. The Thundercats set out to search for their time capsule.

The Mutants, once again searching for a way to destroy the Thundercats, recover some more items from their spaceship. They take their ship's engine and convert it into a giant fireball-shooting machine. The mutants terrorize Third Earth with their fireballs, until the Thundercats go to castle Plunn-Darr and destroy their dangerous new weapon.

Mumm-Ra tricks Lion-O into using the Sword of Omens against Tygra, causing the blade to break in half and lose its powers. The only way Lion-O can restore the Sword is to venture into a volcano and have the Inflamer reforge it. But the Inflamer requires a payment of gold... Has Lion-O taken on more than he can handle?

Mumm-Ra creates device that can make Panthro clones. He embeds the spirit of Hammerhand into his clone and sets it free to destroy Third Earth. The Third Earth inhabitants blame the Thundercats for the terror because they think its the real Panthro destroying their villages and burning their crops. The real Panthro finally encounters his clone and, with the help of Lion-O, manages to destroy it. Enraged about his defeat, Hammerhand destroys Mumm-Ra's cloning device.

Wilykit and Kat accidentally free an ancient monster that was banished to an old shrine centuries ago. The evil monster, Mongor, begins to destroy the planet, and is much stronger than the Thundercats. He captures all the elder Thundercats with his powers. Wilykit and Kat return to the shrine to find a way to destroy him. They report back to Lion-O and tell him that in order to destroy Mongor, he has to fight the monster without looking at it. Lion-O defeats the monster and all is returned to normal.

The Thundercats briefly show Lion-O how the time capsule they recovered from the caveman works. Curious to see more, Lion-O activates it during his night-time watch, and gets caught in its projection rays. The rays send him back in time to Thundera, just before the final tremor that destroyed the planet. Meanwhile, the Mutants have built an evil robot monster that is destroying Cats' Lair. Back on Thundera, Lion-O encounters his father, Claudus, and saves him from a Mutant attack. In return, Claudus gives Lion-O the plans to the robot that was attacking the Thundercats in his own time.

An old scientist seeks the Thundercats to help him save the oceans of Third Earth. Long ago, a crack was made in the bottom of the ocean which caused the water to drain into the earth's core. Dr. Dometone created a plug which sealed the hole in the ocean, and saved Third Earth from destruction. Now, an evil miner, Scrape, has come to remove the plug and mine the rock that is found on the bottom of the ocean. The Thundercats join Dr. Dometone and his frog-like robot, Herkie, to save the planet from total destruction.

Jaga is captured by Nemex, an evil being in the Astral World, and Lion-O tries to find a way to rescue him. Third Earth legend says that the only person who can transport anyone to the Astral world is the evil Nether-Witch. Little do the Thundercats know that Mumm-Ra and the Nether-Witch are one and the same. Mumm-Ra traps Lion-O in the Astral world, and Lion-O sets out to save Jaga. While escaping the Astral prison, Lion-O and Jaga save an old sorcerer named Brodo who has been imprisoned in the Astral Prison for centuries. As thanks, Brodo sends Lion-O back to his own dimension.

The Thundercats think that Snarf is getting too old, and that he is not up to doing as much as he does. To prove them wrong, Snarf saves the Thundercats from another mess. The evil Crystal Queen, Tartara, captures the Arrietta bird, whose songs enchant the Berbils' harvests. Lion-O, upset with her selfishness, goes off to save the bird, but gets caught and put under an evil spell. Snarf, managing to slip through the crystal queens defenses, saves Lion-O and frees the Arrietta bird.

An evil hunter lands on third earth in search of prey to hunt. His holographic machine can tell him about all of the Thundercats, including their strengths and weaknesses, and he is able to hunt down each one of them and put them in Thundrainium cells. He captures all of them but Lion-O and Snarf. Jaga warns Lion-O about Safari Joe before he sets out to save his comrades, and Lion-O is able to defeat him and release his friends.

Nearly all the Thundercats have been captured by the Mutants and imprisoned in Mumm-Ra's Pyramid, forcing Snarf to use his own talents to free them.