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.
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.
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.