Unfortunately, the dark god Unicron heard Primus's waking scream, and immediately moved to attack Cybertron. He reached into an alternate timeline, and kidnapped the Galvatron there using his newly-created minions Hook, Line, and Sinker. Forcing Galvatron to do his will, Unicron sent him to Cybertron ahead of him to clear away any resistance. Pretending to obey him, Galvatron attacked Xaaron's Autobase, then pursued Xaaron into the depths of Cybertron. Figuring that inside the body of Primus, he would be safe from Unicron's eye, Galvatron convinced Xaaron to wake Primus. At this point, Hook, Line, and Sinker found Galvatron and attacked him. Galvatron killed Line and Sinker, but Hook was killed by the newly- woken Primus, who had now taken possession of Xaaron's body. Believing the time was right, Primus transported all the Transformers on Earth to Cybertron in preparation for battle.
In Xaaron's body, Primus told the Transformers he had gathered the story of Unicron and himself. Optimus Prime noted that Primus had a tendency to use them as though they were merely unliving pawns. He was about to mention that to Primus, but that was when Unicron arrived. Primus attempted to fight Unicron, but he was killed in the battle. Xaaron, presumably, was also killed.
Emirate Xaaron was introduced in the UK 1986 annual story 'And There Shall Come a Leader'. He was the most outspoken supporter of transferring command of the Autobot army from the Council of Autobot Elders to a single commander, so that they could fight Megatron's advance towards Iacon like warriors and not politicians. Eventually High Councillor Traachon was convinced, and so Optimus Prime became leader of the Autobots.
When the Ark crashed on Earth with Megatron and Optimus Prime on board, and Shockwave was also lost, the young War-Lord Trannis took command of the Decepticon army. He took back all the cities Prime had liberated, and when Iacon would not fall he levelled it. The Council of Elders surrendered and were summarily executed, with the exception of Xaaron, who had fled with a hundred followers to form the Autobot resistance movement.
Xaaron sent his elite commando team, the Wreckers (The leader Impactor, Rack'n'Ruin, Roadbuster, Whirl, Topspin and Twin Twist) to assassinate Trannis. This they succeeded in doing, but Xaaron soon lost the advantage when a greater tyrant, Straxus, rose to take his place. As the founders of the Cybertronian Empire left the planet for parts unknown, Xaaron's men were forced back into hiding. They waged a guerilla war from a number of Autobases, commanded by the likes of Fortress Maximus and Perceptor.
In 1986, shortly after learning of the renewed war on Earth and the apparent death of Straxus at Blaster's hands, Emirate Xaaron planned a new uprising on Cybertron, codenamed Operation: Volcano. Ultra Magnus and the Autobot Triple Changers were created specifically to fight alongside the Wreckers. Ten of the Decepticons' deadliest killers were to be eliminated. The plan failed because six of them (Ramjet, Thrust, Dirge and the Insecticons) were summoned to Earth by Megatron. One of the remining four, Macabre, had a clear shot at Xaaron in the confusion. Because Ultra Magnus was on Earth battling the future Decepticon leader Galvatron, Impactor took the shot meant for Xaaron and died as a result. Springer took over command of the Wreckers.
Later that year, Optimus Prime and Megatron were accidentally transported to Cybertron. The Wreckers almost executed Prime as an imposter, but Emirate Xaaron recognised his old friend. Prime returned to Earth soon afterwards.
In 1988, Xaaron and the Wreckers were captured by Flame, a mad Autobot scientist, once on the Council of Elders, who had discovered Megatron's prototype planetary drive. He used the remote-controlled corpses of fallen Transformers to clear the city of Kalis, which would be destroyed when the drive was activated. The Autobots were freed by Ultra Magnus and the Sparkabots, and the reanimated Impactor gave his life once again, to kill Flame and keep the reactor from destroying Cybertron. During this incident, Xaaron tried to transform to his battle mode, an act which might have killed him as his old circuits had not done this for so long. In the end it proved unnecessary (and as a result, the transformation was not performed). Trypticon and Flywheels fought alondside the Autobots in this battle.
In 1991, Unicron approached Cybertron, and nothing stood in his way until Emirate Xaaron, prompted by an alternate-universe incarnation of Galvatron, awoke Primus, who slept at the heart of Cybertron. Primus communicated with the Transformers and fought Unicron using Xaaron's body as a vessel. In the battle, Emirate Xaaron was destroyed.