Metroid Prime: Into Darkness is a story written by Metroid Prime. It takes place during Magical Mystery Cure, the Friendship is Magic season 3 finale, and involes the Ing from the Metroid Prime trilogy invading Equestria.
The story begins with an introduction of both Equestria and Aether. It then shifts to Princess Celestia delivering a package to Twilight and reassuring Luna that she was ready. The scene shifts again to a Leviathan floating through space, eventually impacting an unknown area in Equestria. Said impact revives the ancient dark creatures known as the Ing into a dark version of Equestria and its world. The scene then fast-forwards to Twilight's corornation. As she is about to take off for the first time, a dark portal appears. Twilight hesitates and an Ing tentacle reaches for her.