22 in-game years have passed since the Time Twister imploded. Cortex has been banished to another dimension. The world is safe... for now. The Rainbooms still don't know where their friend, Sunset Shimmer, is and set off to find her just when a series of quantum rifts start appearing out of nowhere.

Now they must help reunite the four quantum masks and find Sunset Shimmer before Cortex's newest scheme to rule over time and space causes history in several universes, including their own, to change forever.