Alpha Trion was one of the Primes, the first Transformers created by Primus, participating in the war against the Quintessons. After thousands of cycles of fighting, the principle aid of the Primes, Sentinel, intercepted a transmission about a meeting of Quintesson commanders. The Primes chose to take on the mission themselves and met Sentinel in a cave only to be ambushed by Quintesson Soldiers. The Primes nearly triumphed over their attackers until Sentinel revealed himself as a traitor and turned on the Primes. As the tide of the battle turned, Alpha Trion sent out an urgent SOS message, calling on the High Guard to come to his location before the Primes fell. While the other twelve perished, Alpha Trion fell into stasis lock. Fifty cycles later, the beacon containing Alpha Trion's message ended up lost in waste disposal, but a local disposal worker B-127 salvaged it and used it as a component to make an imaginary friend named "Steve." There the message remained for the next 50 cycles, until Orion Pax and D-16 were thrown into the disposal area B-127 worked in. Orion inadvertently discovered the beacon and activated the message, leading the three to believe it led to the location of the lost Matrix of Leadership and embark on a quest to discover it.

When the three bots (now joined by Elita-1) discovered the cave where the slain Primes lay, Orion found Alpha Trion buried under an immense amount of rock and still lived, reviving him with an energon cube. Alpha Trion reacted violently at first, momentarily believing he was still in the midst of battle, but Orion was able to calm him down and bring him up to speed on the current state of affairs. However, when Orion mentioned Sentinel Prime, Alpha Trion was quick to point out that Sentinel was not a true Prime. Educating the quartet about Sentinel's treachery, he took them to an overgrown cliff where they watched Sentinel kneel before a Quintesson High Commander. Though the four younger bots were dismayed and dejected to learn the truth about Sentinel, Alpha Trion rallied them to action with some wise words, reminding them that they must inform the public of the truth and bequeathing them with the transformation cogs of four of the Primes.

Unfortunately, that was when Sentinel's enforcers discovered them and descended on the cave. Alpha Trion told the quartet to flee as he prepared to hold the line, informing Orion that this battle would have to be his so that Orion's time may come later. Though the Death Trackers mocked him and called him old, the ancient Prime was quick to remind them he still had some fight left in him by transforming into his beast mode and swiftly tearing them apart. However, a surprise attack from above by Airachnid caught him unaware, and a captured Alpha Trion was brought before Sentinel. Defiant even in captivity, Alpha Trion engaged in a battle of words against Sentinel, but Sentinel did not take kindly to the old sage exposing the truth with his speeches and killed Alpha Trion with his blade.

In death, Alpha Trion reunited with his brethren in the AllSpark. A vision of Alpha Trion among his fellow Primes later appeared to a heavily damaged Orion Pax as he fell into Cybertron's core, announcing that he had been chosen by Primus to carry the Matrix and lead Cybertron. As the power of the Matrix reformatted his body, Alpha Trion bestowed upon him the name Optimus Prime.

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