After the Changeling Invasion, Equestria gets the famous Ben Tennyson and his friends over to their world as they were suddenly shipped here by unknown forces believing they were supposed to be dead. Princess Luna starts acting more aggressive and isolated jeopardizing the upcoming Summer Sun Celebration, but what everyone on the surface world does not know is that a sentient piece of Nightmare Moon seeks a return to the real world and plunge it back into her everlasting night.

Evil monsters start terrorizing the citizens of Equestria under the order of an old familiar evil lurking in the shadows looking to take back what is theirs by force. This calls for Princess Luna to call in the teen mystery-solving agency of Mystery Inc. as they agree to help Equestria fight off the incoming threat by exposing the frauds and stop evil from reigning over the land.