This story is a sequel to The Doctor Whooves Chronicles Episode 1: Derpy

The Doctor and Derpy arrive on the Moon in the distant future to find that ponies have set up a massive colony there. However, something dark is lurking deep within the crust of the Moon and it vows vengeance on a certain Princess Luna.

This story is a sequel to Doctor Whooves Episode 14: Work of Fiction

The Doctor, Twilight, and Derpy finally arrive in the Doctor's universe, and just in time for Christmas. The Christmas cheer ends, however, when a group of odd enemies attacks a cozy country hotel. In order to defeat these strange foes, Derpy will have to face something from her past and Twilight will have to help the Doctor reunite with a lost friend.

The Doctor suddenly finds himself in the world of Equestria following his TARDIS accidentally passing through the void. He tries to head back to his universe, but things get complicated when a pegasus named Derpy finds her way into the TARDIS and they end up traveling back to Equestria's distant past.

Rainbow Dash wakes up with a searing pain in her head fifteen days after a serious accident. Her friends tell her that she was in a coma but a series of strange visions make her think otherwise. Why does she know of things that don't exist in Equestria and who is this man that keeps appearing in her dreams? Only a certain princess holds the key to Rainbow Dash finally finding peace.

This story is a sequel to Doctor Whooves Episode 13: Clockwork and the Doctor

The Doctor, Twilight, and Derpy head off to the Doctor's home dimension, but something goes wrong and they instead end up in a dimension where they were merely fictional characters in television shows. Things get even more complicated when they end up separated at a certain My Little Pony convention alongside two fans and a mysterious figure with an odd arsenal of powers appears.

This story is a sequel to Doctor Whooves Episode 12: A Dalek in Celestia's Court

The Doctor has been living in Ponyville for several weeks now and Hearth's Warming Eve is just around the corner. However, the peace is shattered when a mysterious stallion from another dimension named Clockwork appears. As the a dark nightmare wreaks havoc, Twilight is forced to examine her true feelings for the Doctor and Clockwork must face the fate of his wife, Twilight Sparkle.

This story is a sequel to Doctor Whooves Episode 11: Parents' Day

The Doctor, Twilight, Derpy, and the others return to 1002 and arrive right in the middle of Canterlot a mere five minutes after their original departure. They arrive to find a troubled pair of alicorn sisters and an eccentric stallion who knows the Doctor well. However, they also come across a Dalek who has named Princess Luna as its next target.

This story is a sequel to Doctor Whooves Episode 10: The Magician and the Angels

The Doctor heeds to Applejack's request and has the TARDIS take them to July 6, 996. It quickly becomes apparent that Applejack has a plan to change a certain event that occurred on this day. But her choice to attempt to change her future could very well lead to the destruction of the entire universe.

This story is a sequel to Doctor Whooves Episode 9: Triple Rainbow

It's been a month since the Mane 6, Derpy, and Spike started traveling with the Doctor. Things suddenly take a turn for the worse when a foil from Twilight's past mysteriously appears in the TARDIS and they all end up trapped in a seemingly-abandoned asteroid base that has a bad infestation.

This story is a sequel to Doctor Whooves Episode 8: Maiden Voyage

The TARDIS brings the Doctor, Twilight, Derpy, and the others to the Griffin Kingdom in the year 1021. Here they meet a 38-year-old Rainbow Dash training for the Gailenean 1000. Meanwhile, a third Rainbow Dash from an alternate reality appears but with much darker goals in mind.