The world of equestria has been at peace for a long time, however that is all about to change. Queen Chrysalis with her changeling army along with king sombra have returned. They have taken over canterlot, captured Princess Celestia, and cause an uprising in the pony world. Twilight along with her friends and Discord take the elements of harmony and try an all out assault on queen chrysalis and king sombra. Though they fought with power they were no match for the combined powers of the two villains.

With that princess celestia is still trapped in her prison, rainbow dash, fluttershy, and pinkie pie are beaten and at mercy of king sombra, discord's powers are drained by the changelings, and twilight's forehead starts to bleed and she is blown out of the stain glass window. She then has a near death experience and just when she slips out of consciousness she is saved by princess luna and her brother alicorn, Prince Staller. With that said and done they take twilight back to the base camp with discord following behind and rarity and applejack wait for them. When they return, Twilight is rushed quickly to medical help while luna and staller tell everyone the news.
Now that twilight is hooked up to life support, discord's powers have been drained fully, and luna grieving for everyone, things seem grim for everyone. Prince staller then shows shining armor and princess cadence to their little sister, as they are now in tears from her condition staller leaves them to their grieving. Applejack, rarity, and staller try to think of a way to strike back at chrysalis and sombra, discord then reminds them that they are low on medical supplies and unless they know of a place with more to move to, twilight's condition will keep getting worse until she eventually dies from her inability to breath properly.
Staller then reveals to everyone that he and luna know one place with enough supplies to last them five years, he agrees to show them for everyone's sake. Shining armor and cadence help to move their little sister to the base. When they arrive, they find it hidden behind a giant mountain, and only alicorns can sense the secret entrance. Because luna is still feeling guilty, cadence helps staller move the secret wall and get twilight to the medical room. Twilight finally gets the respirator that is fully functional. Applejack and Rarity remind everyone they still need a plan to save everyone from chrysalis and sombra.