Cortana, utilizing the Guardian's Forerunner technology, has traversed backwards in time to assimilate Earth's AI before the UNSC exists. Blue Team and the Arbiter, following them through a slipspace rupture, must stop Cortana before their time is rewritten and erased.

A malignant uprising against Arceus has started a massive war between all Legendary Pokemon. Not convinced they can win this by themselves, Rayquaza requested the assistance of three normal, yet powerful Pokémon. Will they be enough to stop Darkrai and his forces of destruction?