Skeletor and Quakke find a crystal on Denebria that makes Quakke stronger. Quakke tests his new strength on He-Man, Hydron, and Flipshot during their trip to get oil for the Vasionic Resonator on Denebria and they are saved by Sagitar.

During his fight with He-Man, Slush Head destroys the Trithuseum generators on Primus that prevents its core from overheating. The crystals needed to help power the Trithuseum generators upon its rebuilding can only be found in Gorn City on Denebria. He encounters the trader Meliac who Skeletor uses in his plot to defeat He-Man.

The Galactic Guardians and the Evil Mutants remember their recent battle in the Quagmi Swamps. Each side recaps what happened during the battle.

A bug on the Starship Eternia causes it to land on Denebria. Sagitar rescues a Mutant named Felca who is the future bride of Slush Head. Discovering that Sagitar rescued Felca, Slush Head agrees to help the Galactic Guardians get a new part for the Starship Eternia. Flogg finds out that Slush Head invited the Galactic Guardians to his wedding as Skeletor sees this as an opportunity to get rid of them once and for all.

At the advice of Flogg, Quakke puts up bounty posters for He-Man's capture as the Evil Mutants and the Zeps look for him. He-Man frees some prisoners from Slush Head as they join up in his resistance. When Skeletor threatens a village, He-Man offers to surrender if they spare the village.

As the Scientists of Primus work on a way to deactivate the Zeps, Adam and Mara go to where Master Sebrian, Hydron, and Flipshot are being held and free them despite interference by Crita, Slush Head, and the Mutant Troopers. Afterwards, He-Man and Master Sebrian provide a diversion for Skeletor while Mara, Hydron, and Flipshot retake the Starship Eternia.

After the Galactic Guardians capture Quakke and B.H., the Scientists of Primus create a machine called the Mutator that can turn any human into a mutant. When it is tested on He-Man so that he can spy on Skeletor, it changes more than his appearance as destroys the Mutator and rescues Quake and B.H. Not realizing that the mutant is a transformed He-Man, Skeletor names him Cruncher and takes him in storming the Inner Council's chambers.

Master Sebrian and Mara crash land in a remote area of Denebria. When He-Man arrives on Denebria to save them, he encounters some friendly Mutants who claim that they were once humans.

Flogg has obtained some new laser cannons with their range being a threat to Primus. Now He-Man and the Galactic Guardians must infiltrate Nordor and destroy the cannons before it can be used on Primus.

At the advice of Skeletor, Flogg contacts Master Sebrian and gives Primus some Zeps as a goodwill gift for peace between Primus and Denebria. Once Primus is filled with Zeps, Skeletor and Flogg activate their remote that turns the Zeps into hideous beasts that attack the Primans. He-Man discovers that the Zeps are actually androids and that there are too many for him to fight all at once.

Primus has been taken over by the Evil Mutants and the Zeps. As He-Man and Mara have the key to the shield around Primus, Skeletor has captured Master Sebrian, Hydron, and Flipshot and sends B.H., Quakke, and Staghorn to find He-Man. Meanwhile, the Scientists of Primus work to find what makes the Zeps assume their monstrous forms.

Tricking the Scientists of Primus with an award that will be presented at a space station, Skeletor and Flogg use a robot to have them decode the formula for Energon. This substance is used to melt and destroy planets and the award given to them is filled with it. The only thing that can destroy Energon is a power that is as evil as Energon.

Slush Head captures the Scientists of Primus as they are working on repairing the Trithuseum generators. Upon learning that they built the shield around Primus, Skeletor sends them to the Quagmi Swamp in Denebria. He-Man, Hydron, and Flipshot head to Denebria to rescue the Scientists and get them back to Primus to repair the Trithuseum generators before Primus' core overheats.

Master Sebrian and Adam get a message from the Galactic Council's leader that they will meet on the planet Enoos. The same message meets Skeletor and Flogg as they plan to sway the Galactic Council to their side even by having B.H. fake a hit on Mara that Skeletor will save her from. When this works and the Galactic Council suggests that both planets send delegations, He-Man, Hydron, and Flipshot head to Denebria where they are led into a trap by Slush Head and Lizorr while Skeletor and B.H. secretly have a plan to have an explosive ore burrow into Primus.

Skeletor threatens to destroy Levitan if He-Man doesn't surrender. He-Man disguises himself as a Mutant Trooper to get close to Levitan while having a plan to retake Levitan and all of Primus with the help of the Galactic Guardians and the resistance. Though Skeletor will destroy Levitan anyway even if He-Man surrenders.

A spaceship carrying a little girl arrives on Primus. He-Man and the Galactic Guardians are unaware that the little girl is actually a dangerous cyborg used by Skeletor in his plot to bring down the shield surrounding Primus.

The Scientists of Primus create a Super Computer that would link all machines on Primus and the planetary shield. An exiled computer hacker named Mikros collaborates with Skeletor to place a computer virus called the Argazoid into the Super Computer. To combat the Argazoid, the Scientists of Primus use a shrink ray to shrink He-Man, Artilla, Gepple, and Alcon into the computer in order to keep Argazoid from reaching the Vasionic Resonator so that the Evil Mutants can invade.

In order to bring law and order to Gorn City, Flogg takes Skeletor's suggestion to appoint Flipshot as its new sheriff so that Skeletor can spring a trap for He-Man. Flipshot and Spinwit gain the support of Gorn City's mayor Seeka who has no vendetta against Primus. As Skeletor and the ex-mayor Korac orchestrate events to lure Tyroc and the Ugly Bunch to face He-Man by allowing Byloc to be captured, He-Man gains the assistance of Meliac to help defeat them.

Hydron and Flipshot are sent by Master Sebrian to Eternia to find a champion of good to help them in their fight against the Evil Mutants of Denebria led by Flogg. They have a run-in with Andros and are brought to Skeletor who tricks them into thinking that he's a good guy until He-Man shows up. He-Man and Skeletor's fight is taken to Primus where He-Man proves that he's a good guy by fighting off the Evil Mutants while Skeletor forms an alliance with the Evil Mutants

He-Man saves Grot's garden from an attack by Hoove and Karatti. Meeting Werban in the Oasis, Skeletor tricks him into lowering Onnor's shield of protection so that Hoove can lead the Evil Mutants to invade Onnor under the cover of a peace talk.

Following the failed attack on Onnor, Skeletor sends a hologram calling out He-Man to face him on the Cameroon Asteroid. While He-Man and Master Sebrian are sure it is a trap, He-Man goes anyway. While He-Man is facing off against Skeletor, Hoove and the Mutant Shuttle Pods attack Primus' main radar station while Crita, Lizorr, and Karatti capture Master Sebrian and Drissi.

Drissi and Hydron doubt that Caz can join the Primus Space Force. As Flogg leads the Evil Mutants in the next attack, Skeletor and Quakke capture Caz when he tries to stop them and bring him to Denebria where Skeletor uses a special virus to keep him subdued. He will cure Caz of the virus if He-Man surrenders his Power Sword. He-Man comes up with a plan while taking Grot with him.

After Caz injures his leg pretending to be a Galactic Guardian, the Scientists of Primus give him a high-tech Medi-Suit powered by energy crystals that can help him move around until his leg is fully healed. This Medi-Suit gives Caz some abilities. Knowing that the Scientis of Primus put too many energy crystals in it, Master Sebrian advises He-Man to stop Caz before he gets hurt. Unfortunately Skeletor lures Caz to a trap on the planet Dectis causing He-Man, Sagitar, and Tuskador to go rescue him.

Following a recent fight, the Galactic Guardians reminisce about past battles. In a flashback, it is shown that a transporter ship carrying poison gas was blown off course as Hydron and Flipshot train the Galactic Guardians' new recruits Artilla, Spinwit, Tuskador, and the previously-unknown Sagitar. Skeletor plans to destroy the ship with the Galactic Guardians still on board.

The city of Levitan is in need of more berillium to run its generators. Master Sebrian's old friend Treybius travels to Primus to deliver the berillium where his ship the Star Trader is intercepted by the Evil Mutants. After being rescued by the Galactic Guardians, Treybius accompanies He-Man, Master Sebrian, and the Galactic Guardians to Denebria to reclaim the Star Trader and get the berillium before Levitan crashes to the ground.