Unicron first appeared in our galaxy at the height of the Cybertronian civil war in the year 2005. The Decepticons had established control over the majority of the transformers' home planet, Cybertron, and the Autobots were forced into various bases hidden around Cybertron, on orbiting moons, and on Earth in the Autobot City, Metroplex.

He made his presence know to the humans and transformers by devouring the Autobot's Cybertronian Moonbase 1. Around this time, the current leader of the Autobots, Optimus Prime, had suffered fatal wounds in battle with the Decepticon general, Megatron and had passed on the Autobot Matrix of leadership to a new leader, before dying. Seemingly omniscient, Unicron became aware of this transaction and set a course for Earth.

Meanwhile, the Decepticon lieutenant, Starscream (who was next in command after Megatron), had ordered Megatron's disposal by dumping his still conscious body from an airlock on the way back to Cybertron, along with several other badly injured soldiers. The discarded warriors drifted through space towards a silent, waiting Unicron. Upon their arrival(which Unicron claims to have intended), he strikes a bargain with Megatron to seek out and destroy the Autobot Matrix of leadership, revealing that it is the one and only thing in the universe that can stop him, in exchange for a new body and troops to command. Megatron reluctantly agrees after being briefly, psychically tortured by Unicron. Megatron and his injured officers are given sleek and improved new bodies, along with new monikers and a new ship.

Megatron, now known as Galvatron, sets out to destroy the new Autobot leader, Ultra Magnus, using intel given to him by his new master. Galvatron returns to Unicron after destroying the ship that Ultra Magnus was aboard and is again psychically tortured; this time for his incompetence and eagerness to jump to conclusions. Unicron informs him that Ultra Magnus still lives on a planet of junk, where his ship crash-landed after Galvatron's assault on it. Galvatron is successful the second time. However, tired of his master's cruelty, he instead opts to use the Matrix as a tool to enslave Unicron.

Infuriated by Galvatron's betrayal and arrogance, Unicron transforms into a large, menacing robot and begins to wreak havoc on Cybertron, raking huge fingers across its landscape and shooting defensive airforce units from the sky with eye and mouth beams. An approaching ship full of Autobots, including Hot Rod, is consumed by Unicron.

Eventually, Hot Rod reacquires the Matrix and successfully opens it within Unicron. The unleashed power of the Matrix shorts out Unicron's main processor and he begins to mutilate himself in an attempt to locate and dispose of the body part containing Hot Rod and the Matrix. After the Autobots who were swallowed regroup and escape from his body, Unicron utters his final words, "You cannot destroy my DESTINY!!!", and explodes - The only surviving remnant is his head, which now orbits Cybertron as an eerie reminder to the Transformers of their darkest hour.

Unicron has also appeared in the Transformers Armada Universe. This is however not a different Unicron, There is only one unicron across the transformers Multiverse.

This time Unicron has been waiting thousands of years slowly feeding off the hatred of the Cybertronian Civil war. During Starscream's dying breath he fired a energy beam using all of his remaining energon. However Unicron simply fired a much larger, much faster beam at Starscream killing him. Then Unicron began to activate prompting The Galvatron And Optimus Prime of this Universe to form an alliance to stop Unicron. However their efforts were futile due to unicron's nearly impenetrable hide. Then He retaliated crushing many of his attackers then he concentrated his efforts on Cybertron. However Galvatron and Optimus Prime entered

Unicron in an attempt to stop him, but Unicron imprisoned Both and Gave Optimus the option of merging with him. Naturally Optimus Refused, this prompted Unicron to take control of the minicons who turned on Alexis, Rad, and Carlos. But when the three children reasoned with the minicons they turned on their former master and activated the minicons inside unicron who began to drain the life out of the dark God. Then Galvatron engaged Optimus in a fierce duel but the hatred Galvatron was giving Optimus was reviving Unicron. Galvatron Committed what appeared to be suicide to destroy Unicron. For now.