Transformers Prime

Knock Out is researching Ratchet's Synthetic Energon formula, and is using C.Y.L.A.S. (who is still implanted within Breakdown's corpse) as a test subject. The formula makes C.Y.L.A.S. extremely aggressive, so Starscream suggests injecting him with Dark Energon to make him easier to control. However, the mixture of the two Energons turns C.Y.L.A.S. into a mindless zombie craving fresh Energon, and he wanders the ship infecting any crew member he encounters by draining their Energon. After the incident, Knock Out must give all of his work to Shockwave, and Starscream gets beaten up by Megatron for starting this mess.

The Predacon army is almost fully grown and ready for deployment, but Predaking suddenly surprises everyone by revealing he is able to transform and is more intelligent than first thought. Despite Predaking pledging his loyalty, Megatron still worries that he will eventually lead the Predacons to rebel against the Decepticons, so he plans to terminate Project: Predacon by leading the Autobots to the laboratory and having them unwittingly destroy the clones for them.

Having discovered that the combination of Predacon CNA and Synthetic Energon creates raw cyber-matter (the substance Cybertron is made of), the Decepticons plan to repair the Omega Lock, restore Cybertron and cyberform Earth through this process. While gathering equipment for the project, Soundwave is captured by the Autobots, who take him to their base and try to interrogate him about Megatron's plans, but he deletes all of his information and shuts himself down. Laserbeak eventually finds the base and re-activates Soundwave, who proceeds to capture Ratchet.

The Decepticons hold Ratchet captive, and Megatron attempts to persuade him to help complete the synthetic energon formula and restore Cybertron. Rafael and Wheeljack build a flying drone and attach Laserbeak's transponder (which Smokescreen shot off) to it, in the hope that Laserbeak's navigation systems will lead the Autobots to Ratchet so they can rescue him.

Ratchet reluctantly agrees to help the Decepticons perfect the synthetic energon formula. But once it is completed, he decides he can't allow the Decepticons to have it or finish building their new Omega Lock, so he sabotages the project and tries to escape from the ship. The Autobots launch their drone and Optimus Prime follows it, but along the way he is confronted by Starscream and his armada.

The Autobots storm the Nemesis and try to reach the Omega Lock before the Decepticons can activate it and cyberform Earth. Optimus Prime and Megatron face off in a final showdown, while the other Autobots fight off the Decepticon army and race to secure the lock.