Six years have passed since the second civil war of Equestria. For some, it has been an uneasy peace, and when the mysterious group who call themselves 'the Order' and claim to serve the Goddess arrive on the scene once again, the world is thrown into chaos once more. The Crusaders, along with an enigmatic time traveler called Scratch and his allies, are thrown against fate, and the might of all the Order, and they are among the only ones in the world with a chance to stop their dark designs.

Strange sightings begin in Earth's sky. First a global lights show, then what seems to be an entire small planet in the sky. One scientist, Kurt Maddrey, your average brony and Whovian, soon makes the conclusion that the planet is Equestria. While excited at first, this quickly becomes a fatal problem for both worlds. Will he, along with anyone from either planet that will assist him, bring Equestria home before it's too late?

The world is in bad shape. Rainbow Dash works as a sword for hire alongside childhood friend Applejack, protecting their town and working the farm in peace time. The Lunar Festival is right around the corner, and meeting the Queen's apprentice and 'human weapon' Twilight sets the two- along with the town's noblewoman Rarity, mysteriously powerful townsperson Pinkie and unusually gifted Fluttershy- along a dangerous path between the warring forces of light and dark. It is a path that the six cannot easily remove themselves from, and may walk on opposite sides.

As the story travels down the road set forth by the original Season One, loyalties will be tested, secrets never meant to be known by normal humans will be uncovered, and the very structure of Equestria will be thrown into the balance.