Several decades after the Great War between the Autobots and the Decepticons on Earth, the two factions have disbanded and a three member ruling council rules in place of the absent leaders Optimus Prime and Megatron. An uneasy peace has been created on Cybertron, but the rise of the Combiners threatens to bring it to an end.
The story follows the human girl Yakumo, who awakens from cryogenic sleep in a devastated world destroyed by genetically engineered lifeforms, Enterrans. With the help of a few friendly Enterrans, she goes on a journey to find more human survivors and bring peace between the two factions.
After restoring the world to order, one threat remains for Yakumo and her friends. The cause of the war itself, hidden deep inside a meteorite that crashed at the start of the war, a cause that's about to resurface.