Alpha Trion was originally known as A-3. and was the leader of the original rebellion of the Autobots against the Quintessons, having been urged to do so by a small group of five time-travelling Autobots from the Earth year 2006. He also led the Autobot forces in their first war against the Decepticons, known as the second Great War. It was during this war that the Autobots developed the skill of transformation, so that even though they did not have the firepower of the Decepticons, they had greater stealth skills.

The Transformers lived together on Cybertron by uneasy truce, but then, the Decepticons (possibly those who would become known as The Constructicons) built a new kind of robot - one who could fly in robot mode. That robot became known... as Megatron. One specific young worker robot named Orion Pax adulated Megatron for this power, but when he got the chance to meet his hero, he barely survived the experience. Megatron blasted Pax, his girlfriend Ariel, and his best friend Dion, fatally injuring all of them, and stealing Energon from the warehouse they worked at. It was only thanks to a group of Autobot warriors (actually the time-displaced Aerialbots) that Pax and his friends survived. They were brought to the workshop of a great Cybertronian machinesmith - Alpha Trion (it is possible he may have still called himself A-3 at this point). Trion reconstructed Pax, but when he was finished, he was no longer Orion Pax - now he was Optimus Prime! Ariel was reconstructed into Elita-1, and Dion may possibly have been rebuilt as Ironhide or Ultra Magnus.

Over four million years later, after Optimus Prime and his army were stranded on Earth along with Megatron's forces, and subsequently revived, Elita-1 and her guerilla army of female Autobots revealed their presence to Shockwave on Cybertron. Autobots and Decepticons went back to their home planet, where Prime and Elita were reuinted with their creator, Alpha Trion, discovering for their first time their origins.

When Megatron reconstructed five Earth vehicles to resemble Decepticons, he had to bring them to Cybertron to have them programmed by Vector Sigma, the spherical supercomputer at the heart of Cybertron. He stole the Key to Vector Sigma, and accomplished the goal, even as Alpha Trion proved to late in leading a group of Autobots to the computer itself. When Optimus hit upon the idea to rebuild five Cybertronian aircraft as Earth jet planes, Alpha Trion sacrificed himself, merging his consciousness with Vector Simga, to activate it and allow life to be given to the five warriors, who would become the Aerialbots, the very same Autobots who would soon traveld back in time to ensure the creation of Optimus Prime himself.

When Optimus Prime was restored to life by a Quintesson after his death at the hands of Megatron during the Autobot City Massacre of 2005, he voyaged inside the Matrix and briefly consulted with Alpha Trion's essence as to how to cure the Hate Plague which was sweeping the universe. However, Trion did not know the answer, and Prime was forced to ask the other former Autobot leaders, until he realised that the way to cure the plague was to destroy its madness with the wisdom inside the Matrix.

After releasing the energies of the Matrix, Prime suffered from premonitions, which came true when the Decepticons stole the key to the Plasma Energy Chamber, and used it to release the energy contained within the foundry where the original Autobot bodies were forged. To learn more about the Plasma Energy, Prime activated Vector Sigma with the Matrix, and spoke with Alpha Trion's ghost, who told him that the Plasma Energy itself would be Galvatron's undoing, as it was, when the energy backlash from the chamber sent the Decepticons hurtling through space, never to be heard from again.

When the Vehicon general, Tankorr tried to overthrow Megatron II (the descendant of the original Megatron, who had apparently conquered Cybertron 300 years after the end of the Great War by removing the sparks of every Transformer on the planet, shortly after returning from prehistoric Earth) by using the program from the Key to Vector Sigma to wipe out organic life on Cybertron, he accessed and tampered with Vector Sigma, now known as the Oracle, but there was no evidence of Alpha Trion's personality within it. What has become of him is unknown, but he has presumably joined the Matrix.