"The Secret of Cybertron" was a proposed script by writer Flint Dille and creative director Jay Bacal, hastily produced in a week after they read Ron Friedman's original draft for The Transformers: The Movie and deemed it "incoherent." Although hugely proud and excited about the script they had created, Dille and Bacal were disappointed to discover that executive producers Joe Bacal and Tom Griffin did not share their enthusiasm, and "The Secret of Cybertron" was promptly "filed away".

Details on the story of "The Secret of Cybertron" remain minimal, as the script is lost to the mists of time - Dille believes he may own a copy, but has yet to uncover it. It is believed that at least some aspects of the story made it into the completed movie, although Dille describes the finished feature as "such a Frankenstein of different drafts and ideas and people" that he cannot remember which elements, if any, originated in his and Bacal's script. What is known, though, is that "The Secret of Cybertron" originated the idea of the Quintessons as the creators of the Transformers, which Dille later revived for "Five Faces of Darkness".

As pieced together from different interviews with Dille, the story would have allegedly involved Optimus Prime embarking on a quest to discover the origin of the Transformer race. The titular "secret" would have been that Cybertron itself was a giant robot, and the planet would have been transformed by the Matrix of Leadership to fight Unicron, who was in this draft a weapon apparently created by the Quintessons, intentionally setting up a "brotherly" dynamic between the two planets years before Simon Furman got the idea into his noggin.