The Sorceress realizes her old enemy Morgoth is attempting to return to Eternia. She decides to make a stand, and tells He-Man how her first battle against Morgoth caused her to take up the mantle of Sorceress of Grayskull.
Whiplash gatecrashes a royal party to ask the heroic warriors for help. Skeletor has been overpowered by a creature from another dimension called S'Gora. Worse yet, S'Gora is now powerful enough to take on the Sorceress and conquer Castle Grayskull.
Orko learns his uncle, Montork, has been replaced as head of the Trollan Academy of Magic. He-Man and Battle Cat join Orko on Trolla to find Montorks cocky replacement, Snoob, working with Whiplash and teaching him magic.
Stratos is exiled from Avion after being accused of sabotaging the kingdom's defense shield. During his next attack, Skeletor manages to steal the Egg of Avion and hides it in the Demon Zone with his ally Whiplash.
Once again, Granamyr asks for He-Man's help. The dragons of Eternia are mysteriously disappearing and Webstor and Kobra Khan seem to be behind it. But they're sending the dragons to another world where they're used to battle each other.
The heroic warriors intercept Beast Man while on his way to Eternia's Dark Moon. With Man-E-Faces impersonating Beast Man, they find out Skeletor's warriors are manipulating a war between the inhabitants of the Dark and Bright Moons.
Man-At-Arms has made contact with an immensely powerful yet peaceful alien being known as Om. When King Randor and his subjects welcome Om to Eternos, Skeletor attacks with the help of General Tataran and his Goblin Army. During the mighty battle, Om decides to pit one warrior from each side against each other and chooses He-Man to face Skeletor.
Skeletor kidnaps King Randor, Prince Adam, Teela, Man-At-Arms, and Orko in order to have the Royal Guards become leaderless. But Queen Marlena may prove to be a more worthy leader than everyone else believes.
Prince Glitch of Celasia has joined up with Skeletor's gang to find himself some courage. But he soon wants to get away from Snake Mountain and joins the heroic warriors of Eternia. When Glitch's father comes to look for him, Skeletor convinces the King that Randor is holding Glitch hostage.
Orko tries to prove to Prince Dal that the Eternia Kingdom is a magical place by telling him it is the home a special crystal that can make anyone invincible. Prince Dal hopes to use the crystal to help his father at war.
He-Man and the gang are invited to the Sun Temple to witness the charging of the Sun Stone. But along the way, they meet Prankster, a joker from Orko's planet, Trolla, who keeps causing problems for the gang.
While exploring the desert, He-Man and Orko come across an old temple. While playing with one of the machines, inside, Orko accidentally brings Tamusk, one of Eternia's most admired kings from the past into the present.
Man-At-Arms finds a bracelet adorned by the crest of King Randor's long lost father, King Miro. He joins Randor on a secret mission to search for his the old King, but Queen Marlena sends Adam and Cringer after them in a Wind Raider.
Loos, a blind boy, has always wanted to meet He-Man. So He-Man takes Loos on an adventure to the crystal caves. But after a flash of light temporarily blinds He-Man, it's up to Loos to get them safely home.
When Orko uses his magic to restore the Wizard Kothos to human form, he captures the heroic warriors and contacts Skeletor to exchange them for Evil-Lyn, who was the one that turned him into a sand-slug.
When Orko plucks the fabled Bitter Rose as a gift for Dree Elle, Rose Mountain starts to crumble and threatens to destroy the village of the Insect People. Now aware of it's power, Skeletor also wants to get his hands on the Rose.
Orko's old friend Squonge from the Trollan Academy of Magic comes to visit. This Trollan has a tendency to tell tall tales. When he is the first to notice the arrival of the dangerous Slavemaster on Eternia, nobody believes him.
He-Man and Man-At-Arms are invited to Darksmoke and Orko tags along. But the evil dragon Morningstar steals the magic flame of Granamyr and blames the Eternians to start a new war between Dragons and Humans.
Evil wizard Hexon has stopped time so he can become the new Emperor of Simbar. But Princess Kathay, daughter of the current Emperor, sets out to find the Sands of Time and soon receives help from He-Man and friends.
Beast Man and Trap-Jaw have acquired the Amber Crystal of Milaka and decide to go into business for themselves. After conjuring up a fortress, they summon Orko by magic and hold him to ransom. Meanwhile He-Man & Man-At-Arms travel to the original owners of the Crystal, the insect like Polti.
Two Earth astronauts on a mission to destroy a magnetic meteor about to collide with Earth are sucked into a time portal and end up near Eternia instead. To complicate matters, Skeletor seizes the missile intended to destroy the meteor and attempts to use it to blow up Castle Grayskull.
Evil-Lyn plans to magically disguise Kobra Khan so he can infiltrate Eternos on Eternia day, and Skeletor makes sure Orko won't hinder them by getting rid of his magic powers. He-Man and Orko travel to the Magic Falls to get them back.
Lady Arvela strikes a bargain with Angast, King of the Realm of Evil to free her father from Angast's grip. In order to do so she kidnaps the Starchild who is visiting the Royal Palace. He-Man goes after her with Starchild's guardian Bowena as well as Orko who is disguised as one of Bowena's arrows.
Skeletor orders Two Bad to capture Zagraz the comet keeper so he can force him to direct his comets to destroy Castle Grayskull. Soon the comets are causing trouble all over Eternia without Zagraz' direction.
The alien Bendari select two warriors to pit good against evil. Because Adam is prevented from turning into He-Man in time, Fisto is chosen as the heroic warrior. Meanwhile, Skeletor has amplified Spikor's evilness to make sure he won't be chosen himself. During the game however, the evil warriors are allowed to cheat while the good must try to win without resorting to such tactics.
Skeletor plans to replace his Beast Man with the evil inventor Maddok who has built a machine that can digitize wild animals and have them appear in another place, such as during King Randor's birthday celebrations.