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).

This story is a sequel to Doctor Whooves: Invasion of Manehattan

Starlight Glimmer has succeeded, she has managed to steal one of the Star Swirl spells from the forbidden section of the Canterlot library and, after months of work studying countless tomes of arcane magic related to time, she will be able to defeat that princess of friendship and her friends before even meeting her.

All she has to do is stop the brat that was Rainbow Dash from doing the Sonic Rainboom on her. But before she does, somepony stops her and asks her a simple question, 'are you sure you want to do that?'

A dalek appears in Equestria - not just any dalek, but the one that had been corrupted by Rose Tyler's DNA. It has a choice of life as a pony, or dying, and finds that it cannot bear to die a second time. Thus begins a strange adventure as the dalek tries to find a place for itself in a world that is completely antithetical to its former existence and way of thinking...

...and why does that earth pony stallion look familiar...?

Typical stallion, can't multitask. Can he talk and listen at the same time? Derpy wants to know.

Note: Got the inspiration for this story when I was having a chat with my flatmates. The lads and I agreed that we can barely multitask. 😅

Cover art is by askclockwisewhooves on Tumblr. Not sure though, I screenshot'd it from a .gif I found on Google Images.

Part One of the Lynchpin Quintet.

Time Turner is a watchmaker in Ponyville, but he's always dreamed of adventure.

His prayers are answered in the form of a strange being known as The Doctor. But what could his appearance and that the strange machines that he followed here, mean?

This story is a sequel to Doctor Whooves: Birth of the Doctor

Part Two of the Lynchpin Quintet.

The Doctor, Applejack, and the Cutie Mark Crusaders land in Minos, the Nation of the Minotaur, three thousand years in Equestria's future. They find the country embroiled in a war that could threaten to destroy both factions.

One Minotaur has an idea. An idea all to familiar to the Doctor.

Does he have a right to interfere? Does he have the right to stop them if they go to their fate willingly?

And what does this mean that it happened almost the same way in three different Universes.

Proofread by Ephraim Blue

Cover Art by Sweetstrokes

This story is a sequel to Doctor Whooves: The Ultimate Upgrade

The Doctor lands in Canterlot on a certain Alicorn's wedding day.

Now he must find a way to accomplish his goal without breaking the first law of time. Which is even more difficult when he realizes that he isn't sure what his goal is...

And to complicate things even more....

The Master has come to Canterlot

Proofread by Ephraim Blue

Art by Fonypan

The Doctor finds something to do while Derpy is asleep.

Note: Was looking through the list of Genres. Thought I should write a truly [Random] story.

Cover art by askclockwisewhooves on Tumblr.

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

One day, over a plate of burgers, the Doctor and Derpy became very interesting to a lecture group of 4th dimensional beings.

Note: A bunch of nonsense I've come up with after looking at the picture used as the cover art. I don't even know which reincarnation the Doctor is in this story.

Cover art is by askclockwisewhooves on Tumblr. Not sure though, I found the picture on google images in the first place.