After years of failure, and the planets' power sources gone, Dr Cortex and his many creations decide to use the power sources from another dimension, until they are strong enough to return and conquer Earth.

After 2 months of peace, Crash and his friends decide to discover why things are so quiet, only to end up travelling to the same dimension, where they encounter strange multi-coloured talking ponies.

Believing that Cortex is here in Equestria, Crash and his new friends must travel across the land, to do what they do best, find Crystals and prevent Cortex from taking over the world.