Captain Hydron and Lieutenant Flipshot travel across time and space to Eternia to find a legendary hero to help them in their battle against the Evil Mutants. The return home to Primus accompanied by two Eternians: He-Man and Skeletor.
Skeletor has the Mutants destroy Primus' Trifusium Generator, knowing that He-Man will have to travel to Denebria to obtain Trifusium Crystals in Gorn City. Hydron and Flipshot are excited to use an old Starship for their trip.
Only the four scientists of Primus are able to fix the Trifusium generator, so the Mutants decide to kidnap them and take them to Slush Head's home, the Quagmi Swamp on Denebria.
Skeletor pretends to talk peace with Werban of Primus, but manipulates him into lowering the planetary shield instead so the Evil Mutants can attack the cities of Onnor and Levitan.
He-Man accepts Skeletor's challenge for one on one confrontation on Cameroon Asteroid, certain that the Scientists' latest invention will warn the Guardians of any approaching attack on Primus. But then the detector breaks down.
Skeletor's new pet Grr finds a giant crystal hidden in the moon of Nordor that grants great strength for a limited period. He-Man travels to Nordor alone to face his old enemy and destroy the crystal.
When painted animals start to come alive and attack several locations on Primus, He-Man suspects that the artist Helm from Darius-7 has something to do with it.
The Galactic Council demands peace negotiations between the people of Primus and the mutants of Denebria on the moon of Enos. He-Man is skeptical but Skeletor sees many opportunities coming his way.
Caz doesn't want to be a shepherd anymore and insists on joining the Primus Spaceforce. Flogg and the Mutants attack Primus without Skeletor and Quakke, who decide to launch a sneak attack of their own.
Drissi invites the West-Star Space Rodeo to be the special guests at the Festival of Lights. Skeletor and the Mutants befriend Buck West-Star first so they can infiltrate the festival disguised as Intergalactic Cowboys.
Master Sebrian accepts Flogg's offer of peace which comes in the shape of cute and cuddly Denebria animals called 'Zeps'. The animals are a big hit and soon everyone on Primus wants one, even though He-Man remains skeptical.
The Mutants have conquered Primus. He-Man and Mara have escaped with the key to the Vasionic Resonator. The Scientists also manage to sneak out into the Wilderness to get their hands on a Anadroid for experimentation.
Adam and Mara break Master Sebrian, Hydron and Flipshot out of the Evil Mutants' prison (with a little help from He-Man). However, Skeletor has hidden a Micro-Com in Sebrian's robes to track them to their secret hideout.
Skeletor demands that He-Man surrenders himself, or the Mutants will use the tractor beam on their Mothership to pull the floating city of Levitan into space.
The Evil Mutants have taken over the prison ship Gaolotia and lure Caz and Drissi there, knowing He-Man will follow. Skeletor also makes sure that Xenon's Comet is on a collision course with the Gaolotia.
He-Man wants to infiltrate the Mutant's headquarters, and turns himself into a mutant using the Scientists' new Mutator machine. But in doing so, he loses his identity and soon joins Skeletor's side, who renames him 'Cruncher'.
Adam helps Hydron and Flipshot rescue a young alien girl named Vadora, who has lost her home and parents to the evil mutants. Werban becomes her guardian, but all is not as it seems.
An old Priman Western hero called Dukan is revived from a Hibernation Capsule. Determined to prove he can still make a difference, Dukan accepts Skeletor's challenge to meet him in an Abandoned Mining Town on Denebria at High Suns.
The Scientists have created a Master Computer that will connect all of Primus' machines into one interlinked system. But the disgraced Priman hacker Mikros puts a living virus into it for Skeletor.
Using the new Brain Wave Detector, Skeletor records an image of He-Man's brainwaves so he can keep track of him at all times. But when the Mutants capture the Starship Eternia, they are surprised to find no sign of He-Man aboard.
The plans for the Reverse Gravity Generator are stolen by BH and Staghorn (disguised as robots). Skeletor plans to use this machine to push Primus out of it's orbit.
The Mutants make an emergency landing on an asteroid filled with old weaponry, so they disguise themselves as "Professor Galactica's Interstellar Circus" and kidnap the Scientists of Primus to force them to fix all the devices.
The Guardians destroy Flogg's new giant laser canon, but it's wreck emits a green gas that threatens the shield around the planet Primus. Skeletor soon produces more of the gas to weaken Primus and even He-Man's powers are affected.
He-Man captures Skeletor's new Super Computer. Master Sebrian decides to use it to clone the Inner Council, so the original members can take a long needed rest.
Primus is freezing because one of it's three suns is regenerating under a shell of ice. Skeletor offers Transium Ore from Denebria to warm the planet in exchange for their total surrender. He-Man refuses.
After hurting his leg, Caz gets a Medi-Suit to wear which greatly increases his speed and strength. He starts to help Primans in trouble and is soon dubbed 'He-Man Junior', which draws the attention of Skeletor.
The Mutant's vehicles are falling apart, so they contact the Makkina Terrortread Service and ask for new ones. He-Man and Master Sebrian decide to visit the planet Makkina as well to keep an eye on the Mutants.
During a relaxing camping trip, the Guardians reminisce about their first mission involving Artilla, Spinwit and Tuskador, who had been recruited by Sagitar. It involved the container ship Blatazeen 5, it's lethal gas cargo and robot crew.
The deadly gas Black Omega has been detected on Omega-4 and the Primans decide to destroy the entire planet. But they do not realize there is a very active Mutant factory with human slaves on the ice cold planet.