While reading about a strange event in the distant past of Equestria, Twilight believes a Darkness that threatened Equestria once will return. Almost as if on cue, several strangers find themselves on the outskirts of Ponyville, but why are they here?

Sonic and Tails discover that the Chaos Emeralds have sent them to a parallel world. Now they must find the scattered Chaos emeralds and get back home before they are missed. Luckily, with the help of a pony named Twilight and another pony wielding a giant key, they may just find all the emeralds.

Sora, Donald, and Goofy have landed in a new world and have been turned into animals. Sora wonders how the Heartless could invade such a beautiful and peaceful world. When he meets up with a strange blue hedgehog, he is one step closer to unraveling the mystery.

Later, the Doctor, Amy, and Rory have fallen into a strange world where magic is treated like science and everyone, including themselves, is a pony. This is one big wibbly-wobbly timey-wimey situation they have all gotten themselves into.