This story is a sequel to Doctor Whooves Episode 20: The Cure

Discord Whooves and his Cybermen armies have passed through the rift vortex and now nothing in Equestria or beyond is safe. As the battle begins and armies clash, several individuals set out to survive the invasion. And as the Doctor begins to develop a plan to defeat his darker self, he is unaware that Discord Whooves has sinister plans in mind for those close to him.

Traveling between parallel universes is impossible, especially during the process of regeneration, but the Tenth Doctor doesn't have time to question the facts. He's just been thrust through a tear in the fabric of reality, gotten a new body, and landed on a planet called Equestria. Specifically, he's landed in the worst possible place in all Equestria – somewhere that's ready to unleash a “big ol' storm of chaos”.

That's just the beginning of the Doctor's strange new lease on life: there's a whole host of mysteries to explore. Who is Derpy Hooves, the gray pegasus who understands more about him than even she knows how to explain? How does Princess Celestia already know him? And what's the truth behind the Order?

Above all, the Doctor needs to discover if this new universe can heal the wounds he suffered in the last. Only one thing is certain: there's an awful lot of running left to do.

(Warning: For those of you who haven't watched up to the Doctor Who episode 'The End of Time'... spoilers. Also, this story begins between Seasons 2 and 3 of FiM, and things start to... diverge from there.)

Side stories can be found at The Merely Mundane Tales (of a Mad-Pony in a Box).

Everypony knows about Derpy and the Doctor, but not everypony knows how they met.

A time-traveling alien pony.
A permanently cross-eyed pegasus.
A prim and proper cellist.
A hard-working confectioner.
A future DJ with attitude.
An aloof yet friendly lyrist.
These six ponies have been in the background for three whole seasons. Now it's time they got their own story. A story involving secrets, new friendships, and the return of a mare long thought to be an old ponies' tale.
Alternate Mane Six story. Due to five character limit, imagine Octavia tag.

Has an audio reading. Start here

Following the events of "Traveler," Twilight goes to Canterlot to deliver her report on what has transpired since the Doctor's arrival in Ponyville directly to Princess Celestia. She leaves the Doctor in Spike's capable claws, asking him to show Equestria's newest arrival around town while the TARDIS rests and repairs itself from the trials of the previous day.

Although at first distraught at being stranded in the seemingly serene township of Ponyville, the Doctor finds himself reexamining his initial assumptions about the ponies, the land of Equestria, and his compulsive need to travel when he is confronted with the miraculous, impossible events surrounding Ponyville's resident party mare: Pinkie Pie.

The Pinkie Conundrum is the first in a series of continuity branching off from the foundations established by the Doctor Whooves stories: Number 12 and Traveler by the very talented Squeak-anon and all references to these two works of fanfiction is credited to him. Also, while this is a separate continuity from any future works by Squeak-anon, it is strongly recommended to read these two fictions before reading Pinkie Conundrum.

This work has been developed and published with permission and blessing of Squeak-anon, my original inspiration.
Doctor Whooves Intro posted on YouTube by: Cshep99
Cover art provided by FoxInShadow from deviantart.com
Proofreader, Editor and Number One Assistant: 2dextreem

If you enjoy this story as well as my other works, please leave a comment. Constructive critique is encouraged as well as any questions or remarks that may occur.

This story is a sequel to Doctor Whooves Episode 4: Young Armor

The Doctor and Twilight have picked up a mysterious mare named Matilda who seems to know them pretty well. While they try to uncover Matilda's secrets, they find themselves in Equestria 100 years prior to the birth of Princess Celestia. Here they come across a kind and caring King Discord and his wife, Lily, who holds the key to his descent into chaos.

This story is a sequel to Doctor Whooves Episode 5: Before the Chaos

The Doctor finally manages to return Twilight to 1002, only to discover that he's brought her back a little bit late. As the suspicious citizens of Ponyville turn on the Doctor, a strange army led by an old foe invades the town.

This story is a sequel to Doctor Whooves Episode 2: The Awakening

The TARDIS takes the Doctor and Twilight to the planet of Eugora in the year 1899. Here they come across a group of pony soldiers, explorers, and scientists. However, the forests of Eugora hide dark secrets and the Doctor, Twilight, and others find themselves facing off against two deadly enemies, and the Doctor knows one of them.

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.

This story is a sequel to Doctor Whooves Episode 15: The Christmas Ponies

The Doctor, Twilight, and Derpy decide to take Donna to Equestria. However, they accidentally end up in the year 56, where Equestria is currently caught in a bloody war with the newly-founded Changeling Empire. When Derpy and Donna are taken captive, the Doctor and Twilight must team up with a hardened Celestia and a simple farmmare in order to stop the merciless Queen Esmeralda.