Derpy wishes to go somewhere relaxing. The Doctor is willing to grant her wish but the unexpected appearance of a unicorn named Twilight Sparkle and the TARDIS unexpectedly taking them 600 years into the future changes his plans.
The Doctor returns Derpy to her time, but what they find waiting for them is a panicked Carrot Top, a mysterious spaceship, a pair of confused mares, and a sinister creature with a desire for Derpy Hooves.
Following an accident with the TARDIS, the Doctor finds himself in a strange universe with a new body that he didn't gain from regeneration. Meanwhile, a pegasus named Derpy is unaware that her life is about to change forever.
The Doctor and Derpy arrive on the Moon almost 1000 years in Derpy's future. Here, they find a futuristic, Equestrian Moonbase as well as a dark force that has a score to settle with the visiting Princess Luna.
A month after the return of King Dusk, Twilight is still his captive but the Doctor and his allies are planning to infiltrate the deadly land of twilight in order to save her and all of Nymphadora.