The central twist of "Transformers One" is the revelation about Sentinel Prime. He is not a benevolent leader but a traitor who, years ago, made a deal with the alien Quintessons. He murdered the other Primes and seized power, secretly supplying the Quintessons with Energon to keep them at bay. To facilitate this, he created the cog-less miner caste by removing the transformation cogs from bots at birth, ensuring a permanent, subservient workforce.
Upon learning this truth from Alpha Trion, Orion Pax and D-16's friendship fractures. Orion wants to reveal the truth and lead a peaceful revolution, while D-16 is consumed by rage and a desire for vengeance. They are gifted cogs from the fallen Primes, finally allowing them to transform. During the final battle in Iacon, Orion successfully broadcasts proof of Sentinel's crimes. D-16, ignoring Orion's pleas, attempts to execute Sentinel. Orion leaps in the way of the blast and is fatally wounded, falling into Cybertron's core after D-16 lets him go. D-16 then kills Sentinel, takes his cog (which belonged to the legendary Megatronus Prime), and rebrands himself as Megatron, declaring an end to the age of Primes.
However, Orion is saved by the spirit of Primus and the original Primes, who deem him worthy for his sacrifice. He is granted the Matrix of Leadership and resurrected as Optimus Prime. He returns to Iacon and defeats Megatron in a climactic battle but chooses to spare him, banishing him and his followers instead. In the aftermath, Optimus uses the Matrix to restore Cybertron and give cogs to all transformers. He names his followers the "Autobots." In a final scene, Megatron rallies the former High Guard, including Starscream, and names his new faction the "Decepticons," setting the stage for the Great War.