However, a single fragment of that universe was able to escape the destruction, and, being sentient, this fragment was able to use Unicron's sleep to its advantage. During this time, it rebuilt the universe without waking Unicron, and transformed its sentient core into a protector for the new universe: Primus. Unicron eventually woke and immediately began destroying the universe again. Primus fought back, but it became clear that brute force was insufficient against him. Primus then took the battle into the astral plain, but Unicron overwhelmed him there as well. In an act of desperation, Primus suddenly left the astral plain with Unicron in close pursuit. Intent as he was on destroying Primus, Unicron didn't realize that he was being led into a trap. As a result of the act, both minds were trapped inside planetoids.

Soon, Unicron realized that he could psionically shape the metallic mass of the planet he occupied. In time, he changed it into a planet with the following capabilities: devouring whole planets and processing them into energy, independent space flight, nonlinear timestream access, psionic manipulation of metallic masses in the immediate vicinity (down to an atomic level), and transformation into a humanoid mode. Once able to do so, he again journeyed the universe devouring everything in his way.

Meanwhile, Primus had converted his own planet into Cybertron, on which he created the Transformers, intended to be the universe's last line of defense against Unicron. He then allowed them to evolve naturally while he shut himself down to avoid detection from Unicron.

On Cybertron, several million years later, a fight between the Autobots and Decepticons resulted in a stray shot waking Primus, which immediately caused Unicron to track him down. Unicron, knowing that the Creation Matrix was in fact the essence of Primus's life force, sent Hook, Line, Sinker, and an alternate timeline's Galvatron to Cybertron to destroy it before his arrival. Instead, Galvatron turned on Unicron's other servants and helped Emirate Xaaron contact Primus for help. Thus, when Unicron finally arrived on Cybertron, the combined Tranformer army was there to meet him (with a few exceptions). In the resultant battle, many Transformers were killed, but Optimus Prime was able to regain the Creation Matrix from Thunderwing and opened it while inside Unicron. The explosive force of pure good meeting pure evil tore apart Unicron's body, apparently killing him.