Origin #1 (Jetlag Cartoons):
At some point, hostilities developed between Denebria and Primus. Flogg's army was more powerful than anything on Primus, and he took advantage of their peaceful nature and launched a campaign to conquer the planet. However, Primus was protected by a planetary shield, kept up by the psychic energies of Primus's Inner Council. The shield was strong enough to stand up to Flogg's firepower, so he began to focus all of his attacks on the shield, eventually causing it to weaken and crack.
It was at this point that the people of Primus send an expedition to the past to find a hero with 'the power of the good and the way of the magic'. The expedition resulted in the arrival of two warriors from the past, He-Man and Skeletor. Just as the two new arrivals came to Primus, Flogg finally broke through the shield, and personally led an assault force down to the planet. Flogg and his Mutants attempted to attack the Primans, but were driven back easily by the newly arrived He-Man and forced to retreat. Flogg returned to the Mothership, but was joined by the other new arrival, Skeletor. Skeletor offered Flogg an alliance, and Flogg accepted, but wanted Skeletor to remember that he was the one in charge. Skeletor accepted Flogg's terms, and bowed before Flogg.
While Flogg was an effective military commander, he lacked Skeletor's intelligence and cunning. Flogg and Skeletor had an uneasy alliance at first, but Flogg soon came to rely on Skeletor's advice, and the two began to work together effectively as the leaders of the Mutants. Skeletor's plans often relied on manipulation, deception and cleverly thought out ideas, where as Flogg usually preferred to rely on the Mutants sheer brute strength. Skeletor's plans were ambitious, and soon Flogg himself wanted nothing less than to be 'King of the Tri Solar Galaxy'.
Due to a complex plan devised by Skeletor, the Mutants did, at one point, conquer and occupy Primus. The plan had Flogg sue for peace with Primus, and offer the Primans gifts in the form of small, adorable Denebrian creatures called Zeps. The Zeps were, in fact, powerful machines through which Skeletor was able to work his dark magic across Primus. The 'Ana-Droids', as they were called, attacked Primus from within, while the Mutant forces attacked from outside - the Primans were taken completely by surprise, and soon, the planet fell into the hands of the Mutants. Flogg and Skeletor landed on the conquered planet and stormed the council chambers in Onnor, capturing Master Sebrian in the process. Flogg was furious to discover that he still could not destroy the shield, as Sebrian had entrusted the key to the shield to He-Man, who had fled to the wilderness.
Flogg set himself up in Sebrian's home, organising the Mutant occupation of the planet. Soon enough, He-Man had formed a resistance against the Mutants, and Flogg and Skeletor's efforts were devoted to destroying it. Eventually, Flogg and Skeletor used the Mothership's new tractor beam to take the entire city of Levitan hostage, and demanded that He-Man surrender himself, or the city would be destroyed. He-Man finally surrendered at Levitan, and was brought before the Mutants in chains, but before Skeletor could execute him, the rebels made their move and attacked, having found the weakness to the Ana-Droids. The Mutants were forced to retreat to the Mothership, and prepared to tow Levitan into space, killing everyone in the city, but, unbeknownst to Flogg, the rebels had also found a way to reverse the tractor beam. Flogg was shocked when the tractor beams particles started reversing, and the bridge exploded around him - severely damaged, the Mothership was then thrown from the planet, and the remaining Mutant forces were driven back by the Primans. Flogg had been defeated.
Flogg then set about expanding his power base. On Skeletor's advice, he sent Crita to the planet Nekron to assist the evil Gleanons, who were at war with the Mytes. The Mutants hoped to make a deal with the Gleanons and gain control of their transium ore mines. The Mutants also began to attack other planets, such as Danzig and Equinos.
Despite his considerable power, Flogg was still restrained by the Galactic Council, and would often warn Skeletor not to cross them.
Some time later, the Mutants and the Galactic Guardians were summoned to take part in 'The Games'. Flogg, determined to defeat the Guardians in the games, travelled to the planet Crelus to enlist the help of the Yolt, the Blacksmith of Crelus. They fooled Yolt into thinking they were a force good, and he agreed to upgrade their weaponry. Flogg himself was one of the first to recieve a weapons upgrade, and had a powerful grappling hook installed into his armour, replacing his need for a laser whip.
The Mutants, however, lost the games. Humiliated, and having grown tired of Skeletor's plans, Flogg was ready to return to Nordor, but found out that He-Man and the Guardians were detained and imprisoned by the organisers of the games. This left the Mutants with a golden opportunity, Primus was undefended. Flogg ordered an all out attack on Primus, also summoning Crita and the Gleanons to assist in his assault. The Mothership and the vast armada gathered by Flogg overwhelmed Primus's defences, but ultimately, He-Man and the Guardians escaped and returned. Flogg was caught off guard, and separated from the Mothership - with the Starship Eternia hovering in front of him, weapons armed, he was forced to surrender.
Flogg had finally lost, and signed a treaty with Master Sebrian, ensuring peace with Primus. This enraged Skeletor, who was furious that Flogg had surrendered. Flogg blamed Skeletor for his defeat, and attempted to shoot his former ally, however, Crita knocked the gun from his hand. Condemning Crita and Skeletor, Flogg gathered his forces and left in the Mothership. The war was over.
Origin #2 (MOTUC Bios):
Before Skeletor passed through the Laser Gate and arrived in the Tri-Solar System, Flogg the Terrible was the commander of the Horde’s Denebrian Space mutant goon squad. Directing operations either from his secret hideout in a Gorn Crater or from his camp city of Diobo in the Regula region of Denebria, Flogg launched raiding parties on the neighboring planet of Primus in the name of his Horde commanders. A vain and boastful bully, Flogg’s favourite weapon is his laser whip which he calls The Sidewinder. Flogg has a nasty temper and agreed to join Skeletor as his humbled second in command in a secret bid to one day betray him and use Skeletor’s power to take command of the Horde Empire for his own!