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In the Unicron Trilogy universe, Primus was introduced as the living energy core of Cybertron, as well as the originator of the precious and ancient fuel, energon. Transformers of this universe believed the stories of Unicron, Primus, and Omega Supreme to be only myth and legend until the existence of Unicron was revealed in the "Unicron Battles" of 2010. With Cybertron left in a disastrous state after the chaos-bringer's attack, large amounts of Energon were required to repair the planet, and to search for and acquire the mineral, the united Autobot-Decepticon forces entered into an alliance with the Earth Federated Government.
Primus entered into the equation when the project's head scientist, Dr. Brian Jones, brought his son, Kicker, to Cybertron. Terrified of the giant robots surrounding him, Kicker fled, only to find himself tumbling through tunnels into a hidden chamber deep beneath Cybertron's surface. Primus awoke and saved Kicker from what would have been a fatal fall, and for his own reasons, imbued the child with a special gift - the ability to detect energon throughout the universe. He also told Kicker that that he found the boy's species interesting and is curious about them. Optimus Prime subsequently discovered Kicker in Primus' chamber, and the god chose to work with the Transformers quite directly, imbuing them with the "Spark of Combination," which would allow the Autobots to combine and increase their powers. Primus went on to advise Optimus Prime on his actions in order to prepare for the future, including the Terrorcon invasion, the return of Megatron, and the next battle with Unicron; although vague at times, he would offer just enough information to allow his children to survive the threats they faced. Primus was often very weak due to the damage done to the planet's surface, and spent most of his time in a mode of stasis to preserve his energy and keep Cybertron's energy grid online.
When Megatron succeeded in reanimating Unicron, most of the Autobot army was critically wounded in the ensuing battle. This prompted the sleeping Primus to awaken and infuse their armor with his power, upgrading them into new forms, and allowing Optimus Prime and Omega Supreme to combine into a gigantic form and defeat Unicron.Unicron's spark survived, however, and Primus sought to contain it by trapping it at the heart of a new sun that he created from a reservoir of "super energon" hidden within Cybertron.
Primus' plan to contain Unicron's essence in the center of the sun failed when the star collapsed into a massive black hole which threatened not only Cybertron and the universe, but the entire multiverse itself. His energy drained to the point that he had once again been rendered dormant, Primus could now only be awakened and restored to full power by the four ancient Cyber Planet Keys, lost to the far reaches of the galaxy in a failed space bridge experiment eons ago. The magnitude of the threat posed to the multiverse was enough to summon Vector Prime - one of the original thirteen Transformers, who had been following Unicron through the multiverse and repairing the damage he had done - back to Cybertron to aid the Autobots in the quest for the keys.
Eventually, despite continued attempts by both Megatron and Starscream to steal the power of the Cyber Planet Keys, the Autobots were able to gather the keys from Velocitron, the Jungle Planet and Earth, and brought them and their focusing device, the Omega Lock, back to Cybertron. Coupling these three keys with the power of the Matrix, Optimus Prime was able to initiate Primus' transformation from planet mode to robot mode. Communicating with the Autobots through the Mini-Con, Jolt, Primus explained that the destruction of Unicron, the embodiment of the force of evil, had unbalanced the universe, and that only he could seal the black hole and restore order - but to do that, the fourth Cyber Planet Key, from Gigantion, the Giant Planet, was required to reconnect Primus's spark with his body and restore his full power.
Attempting to retrieve the Omega Lock, Starscream made a rather pointless attack on Primus, only to be smacked down hard. Shortly thereafter, when Primus was in the process of channeling some of his power into holding back the ever-growing black hole, Starscream tried again, plunging into the energy beam and absorbing some of Primus' power into himself. Starscream expanded in size until he was as large as Primus himself, but Primus did not take this slight lightly, as he converted Cybertron's moons into a pair of mace weapons and relentlessly pounded Starscream into submission.
Eventually, the Autobots were able to acquire the final key, as well as to reactivate the four ancient ships which had carried the keys to the respective worlds ages ago - the Atlantis, the Lemuria, the Hyperborea and the Ogygia. Primus fused the four ships together to form the Ark, and with his powers subsequently restored by all four keys, he channeled all of his power through the Ark as a beam, straight into the heart of the black hole. With a massive blast, the black hole was finally sealed, and Primus transformed back into Cybertron - not Cybertron as it had been, but a new Cybertron, infused with the differing aspects of Velocitron, Jungle Planet, Earth and Gigantion, a true paradise for Transformers and humans alike.
While the Autobots were occupied with the quest for the Cyber Planet Keys, Unicron's heralds Ramjet and Nemesis Prime arrived on Cybertron, intent on unleashing the Dead Matrix - as the Matrix was the antithesis of Unicron, so too would the Dead Matrix ensure the destruction of Primus, thereby totally destabilizing the multiverse and reducing it to a sea of entropic chaos. For the first time, it would be possible for Unicron to strike at Primus in all realities simultaneously, ending their cosmic feud once and for all.
Ramjet and Nemesis Prime were ultimately stopped by Vector Prime and allies Sentinel Maximus and Omega Prime, plucked from the midst of the Universe conflict by the multiverse-warping energies of the black hole. The Dead Matrix, however, was cast into the heart of the black hole by Unicron's servant Soundwave, freeing Unicron's spark and allowing it to adopt a new, diminutive physical form. Unicron participated in the escalating Mini-Con civil war on Cybertron's moons, but when the planet transformed into Primus' robot mode, Unicron fled. His whereabouts are unknown.