The opening chapter of Scholar Whooves, focused on the Gods, the emergence of new enemies like the Batleks, and the deep lore of the Poniverse. The first five episodes follow the First Scholar, an Earth pony, before the story passes to the Second Scholar, a Pegasus, for the remaining five.

After a pivotal point in time known as the Time War — fought between the Azurians, a Timelord race, and the Batleks — the story turns to recurring enemies and the deepening mystery of Lunar Quils: how he appeared aboard the TARDIS, to the moment he takes in the mind of a Timelord and then forgets the Scholar. Episodes 11–15 follow the Third Scholar, an Earth pony, with the Fourth Scholar, a Unicorn, leading episodes 16–25.

Known as The Fourth Scholar Specials, this set of five special episodes begins with a brown Pegasus — a friend of the Scholar whom he has forgotten. The second explores the origins of the Scholar, including his real name. The third revisits Nightmare Moon and her return, in the spirit of the opening episodes of My Little Pony: Friendship Is Magic. The final two episodes form a two-part story titled End of the Universe.