The Mane Six meet a colt who goes by the name Eon. He's the last celestial pony and has a secret that he's keeping from everyone. As time goes on, an old enemy returns to destroy Equestria and Twilight is receiving troubling dreams about Eon and a shadow dragon. What is Eon hiding from them? Twilight visits Princess Luna and Celestia for some information but even they cannot answer her questions. Something strange is going on in Equestria, and Eon might be the cause of all this. Can the mane six figure out what's going on and save Equestria? Twilight soon gets a visit from a winged lizard named Zhen who warns her that Eon isn't what he seems to be and one of her friends will betray her. Cheibey, a telepathic alien cat, explains to them that the only way to save Equestria is to go into the spirit realm and defeat the shadow dragon called Xanna.

At the midst of all this chaos, Philomena might be the key to solving this giant puzzle.