The Autobots are on the run after the destruction of their base. Meanwhile, military strikes against the new Decepticon fortress, Darkmount, prove ineffective.
The Decepticons breed a dragon in the laboratory using prehistoric remains. The dragon attacks the Autobots back on earth. Ultra Magnus finds the group on earth and fights off the dragon.
Ultra Magnus takes control of the Autobots, sending the dragon to the Arctic and fighting Megatron. Meanwhile, as Optimus fades, he struggles to identify a new Prime.
The Autobots struggle with new team dynamics and Smokescreen begins to regret his decision not to become a Prime. The Decepticons discover Predacon bones on Earth and plan to clone an army.
The Autobots continue to search for Predacon bones. Agent Fowler and June head to a museum to retrieve one, but have an unexpected encounter with Knockout.
Mixing Dark Energon with Knock Out's refined Synthetic Energon formula causes Cylas to develop vampiric capabilities, and soon Knock Out and Starscream find themselves in the middle of a vampire-zombie-robot epidemic aboard the Decepticon ship.
Upon discovering that mixing Synthetic Energon and CNA creates cyber-matter, the Decepticons plan to rebuild the Omega Lock. Meanwhile, Soundwave is captured by the Autobots.
Ratchet agrees to perfect the Synthetic Energon formula, but then begins to sabotage Decepticon plans. Meanwhile, the Autobots use Laserbeak's tracker to find the warship.