Dr. Eggman, with the help of the re-reconstructed Megatron and the human mercenary Silas, produces a clone of Optimus Prime, which Aisling off-handedly names Nemesis Prime, and sets it loose on Cybertron, where it proceeds to wreak havoc. What's worse is that this so-called "Nemesis Prime" is powered by one of the Chaos Emeralds that Bowser snatched in the meantime, giving it the power necessary to replicate the god-like power of the Matrix of Leadership to devastating effects.

When Ratchet reveals the deception of Nemesis Prime's actions to the real Optimus Prime, the Searchers, alongside the real Autobots, band together to try to track down Nemesis Prime and retrieve the chaos emerald.