The Doctor is back, and he must stop a Zygon disease from killing everyone on Earth. With Twilight Sparkle, and Sunset Shimmer at his side, the Doctor has just thiry-six hours before the disease kills him, and everyone on the planet.
Upon returning to Canterlot High after a trip to New York, the TARDIS gets trapped in a temporal schism, causing it to bounce between multiple time periods. With The Doctor trapped in 1991, he must communicate with Twilight over the years.
Omega has crossed Gaea with Earth, creating an unstable planet, and only the Doctor can stop it. But, this time, it will take two sets of elements of harmony, as well as a second Doctor.
It's the holidays at Canterlot High, and The Doctor decides to pay Sunset a visit. However, things turn sour when The Doctor discovers a crack in time leading to Equestria. More importantly, it leads right to a Changeling Hive.