The Galactic Guardians are in need of a trainer for the upcoming mutant invasion. When they arrive on the planet Nekron, they encounter the shady and unusually large Myte named Wulk who trains them until it comes to a certain maze where he has plans of his own that involves working Skeletor to take revenge on the Mytes.
President Pell sends his ambassador Bimo to Primus to showcase his robot Kog. Upon being contacted by General Nifel and Crita, Skeletor and Flogg plan to reprogram Kog to destroy Levitan where they have the Gleanons' programmer Private Dobson do the job. Upon Bimo and Kog's arrival, Optikk activates Kog to attack as he, Staghorn, Hoove, Slush Head, B.H., and Quakke begin their attack on Levitan.
Mara contacts Master Sebrian to inform him of a radio signal from the planet Zil that has been uninhabitable due to the storms there. He-Man and Spinwit head to Zil where they meet their inhabitants who would like Spinwit to save them due to the crystals for their Tornado Machines are almost out of power. Meanwhile, Skeletor takes B.H. and Quakke with him to attack Zil.
He-Man, Hydron, Flipshot, Sagitar, and Mara head to the planet Nekron to negotiate peace between the Mytes led by President Pell and the Gleanons led by General Nifel. They come to the aid of the Mytes when Crita collaborates with General Nifel in capturing President Pell in order to access the Transium Mines and obtain enough to make weapons for the Evil Mutants.
After helping to accompany Hydron, Flipshot and Gepple to study the solar flares, He-Man learns that Sagitar's strange behavior comes from the Running of the Herd vision as He-Man allows the group to head to Equinos to celebrate the Horse Lords' heritage or else perish. Flogg plans to be present at the Running of the Herd with Skeletor, Slush Head, Staghorn, and the Mutant Troopers as a way to target Sagitar while threatening the planet's destruction to General Nekor.
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.
Adam is on trial for running away during an attack by the Evil Mutants and a supposed act of treachery when he was secretly transforming into He-Man with Werban prosecuting him. Despite Master Sebrian attempting to speak on Adam's behalf, Adam is found guilty by Werban and is to be shipped off to the Prison Moon for the next 18 Telks. Meanwhile, Skeletor and Flogg enlist their inside person to plant a disruption bomb at the Titus Observatory to serve as a diversion for the Evil Mutants' next attack.
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.
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.
The Scientists of Primus inform Master Sebrian that a deadly gas called the Black Omega has the power to destroy Primus' planetary shield and is located on Omega 4, a frozen planet at the edge of the Tri-Solar Galaxy. Master Sebrian agrees with the Scientists' suggestions to have He-Man destroy the planet with the Black Omega. When He-Man, Spinwit, and Tuskador on Omega 4, he discovers that there are some inhabitants on Omega 4 enslaved by the Mutant Maxus and his two-headed servant named Zark who were exiled there by Skeletor. Maxus and Zark are using the slaves to harvest the Black Omega in order to get on Skeletor's good side.
An asteroid gets passed Primus' planetary shield. As the lasers from the Starship Eternia doesn't phase it, He-Man heads out to intercept it and deflects it into the sea. Master Sebrian discovers that the asteroid is causing trouble for the underwater city of Serus where Hydron is from. Learning form Hydron's sister Aquata about Serus' flooding, the Galactic Guardians work to seal the crack. Soon, they must deal with the living asteroid Keto who plans to drain Primus of its energy.
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.
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.
Skeletor and Flogg have Primus' planetary shield bombed with everything they got. He places a special super-computer on a shuttle pod which He-Man obtains as the Scientists of Primus discover that it can produce clones. When the Scientists of Primus use it to clone the Inner Council members so that they can rest, Skeletor activates the super-computer where the clones work to disable the planetary shield.
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.
The Galactic Guardians investigate a destroyed ship orbiting Primus and find a Hibernation Capsule containing Dukan who is one of the greatest heroes in Primus' past. Skeletor challenges Dukan to a duel in an abandoned city on Denebria. Suspecting trouble, He-Man, Hydron, and Flipshot secretly follow Dukan.
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.
The Evil Mutants have taken over the prison ship Gaolotia. When Caz and Drissi take an Astrosub and get baited to Gaolotia, Skeletor contacts He-Man telling him to come rescue them at Gaolotia. The Sorceress of Castle Grayskull contacts He-Man stating that Skeletor is having Gaolotia placed in the path of the comet Xenon.
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.
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.
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.
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.
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.
The Festival of Lights is a tradition where a solar eclipse happens to the Primian Suns and a celebration will occur after that where Caz states to Adam that they celebrate the return of the Suns. As He-Man will be attending an interstellar rodeo run by Buck Westar that comes to Primus, Skeletor plans to enter Primus by taking over Buck Westar's ship and capture the Galactic Guardians one by one until only He-Man and Sagitar are left.
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.
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.
Obtaining a painting from a man named Helm, Skeletor and Slush Head stow away on Captain Tipper's ship and heads to a cave in Primus's wastelands and uses a spell to bring the dragon in the painting to life to cause chaos on Primus. He-Man, Hydron, and Flipshot then work to defend Primus from the dragon and other Temperic Oil paintings that Skeletor brings to life.
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.
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.
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.
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