Skeletor saw a rare opportunity for power when warriors from the future named Hydron and Flipshot were captured by one of his henchmen, Andros. Andros informed Skeletor that the two warriors were from an advanced, but defenceless race. They had come to the past seeking a champion for good. Seeking to take advantage of the situation and gain power in the future, Skeletor pretended to be the champion for good that the two warriors sought. His plan had almost succeeded when He-Man arrived and engaged him in combat. With time running out, Hydron and Flipshot were forced to take both He-Man and Skeletor to the future with them.
When he arrived in the future, Skeletor quickly showed his true colours, and formed an alliance with the Evil Mutants of Denebria, who were determined to take over the planet Primus. Skeletor vowed to teach the Mutants how to defeat He-Man and conquer Primus, if they taught him the ways of this new galaxy - the Mutant leader, Flogg, agreed to Skeletor's terms, but Flogg insisted that he remain in charge. Skeletor agreed, and soon began to manipulate Flogg - effectively ruling the Mutants from behind the scenes, and often either using flattery or intimidation to force Flogg into going along with his plans.
Shortly after arriving in the future, Skeletor located an ancient crystal on Moon Nordor which increased his power - following a battle with He-Man, the crystal was destroyed, but Skeletor gained it's power forever, gaining new armour in the process.
With Skeletor's assistance, the Mutants attacks on Primus became more deadly - as he used his cunning to devise carefully constructed plots to bring down the defensive shield around Primus. He also used the fact that he was an unknown element in the future to his advantage; often attempting to make new allies and manipulate others into believing he was a force for good, something which infuriated He-Man. His outwardly pleasent and calm demeanour allowed him to lull others into a false sense of security.
One of Skeletor's greatest achievements was his successful plan to have Flogg sue for peace with Primus, then send in 'gifts' in the form of cute, Denebrian, creatures called Zeps. Unbeknownst to the people of Primus, these were actually robotic creatures, which soon transformed into powerful 'Ana-Droids' - androids through which Skeletor could work his dark magic across the entire planet. With Primus under attack from within and without, the planet ultimately fell to the Mutants, and Skeletor and Flogg seized control of the planet, setting themselves up as it's rulers and imposing a brutal occupation upon it's people. However, much to Skeletor's annoyance, He-Man had escaped into the wilderness, and soon began to lead a rebellion against the Mutants. Ultimately, after several failed attempts to capture He-Man, Skeletor and Flogg held the entire city of Levitan hostage, and threatened to two it into space if he did not surrender himself.
He-Man surrendered, and was brought before Skeletor, who prepared to execute his old enemy before the watching crowd of demoralised Primans, and gleefully told his enemy that despite his surrender, he still planned to destroy Levitan and kill everyone in the city - but the rebellion had found out his Ana-Droids weakness - and devised a way to turn the Mutant's tractor bream weapon against them. Before Skeletor could complete his execution of He-Man, the rebels struck, and the crowds revolted against the Mutants, driving them back to the Mothership. Skeletor was ready to destroy Levitan and everything on it in retaliation, but the Primans used a new weapon to reverse the tractor breams power, severely damaging the Mothership, and blasting the Mutants from the planet. Soon after, the rest of the Mutant forces were driven back, and the occupation was brought to an end.