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...?

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?'

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).

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: 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

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

"So... Doctor... care to take a stroll in our private garden?"
On the run from Gallifrey, the First Doctor encounters Celestia and Luna in the pre-classical era. And the encounter changes the destinies of all three of them forever.

This story is a sequel to Doctor Whooves: You Are Not Alone

Part 4 of the Lynchpin Quintet

Weird things happen in Dodge Junction. This is common knowledge. It's been going on for years.

When the Equestrian Doctor and his companions land however, they meet up with a certain Raggedy Man, who says that he's here to help.

Things are disappearing. No one can remember the town preacher. There is no town doctor.

And Discord himself is present, warning AJ and the Crusaders that the Doctors might be the most dangerous beings alive.

The Doctor must be careful here, a Silence has fallen over Dodge Junction

Edited by Ephraim Blue

Cover Art By: CogWing

The TARDIS, decides she has had enough of the Doctor's moping, and she wants an adventure. What could be better than travelling through the void to a more interesting universe! However, she runs into a snag.
Stuck as a pony of some type, and without her powers of timetravel, how will she survive in this world?
Especially with the natives at war and being particular unhelpful.
A fourth dimensional being like herself will fit in just fine. Right?

This story is a sequel to Negotiations

It's a tale as old as time itself.

A wonderful individual of many faces, a handful of adventurous companions, and a seemingly inconspicuous blue police box.

This time, the Doctor finds himself in a dimension not his own, in familiar lands more alien than the planet he appeared on. Dropped smack dab in the middle of the Conversion War, it's up to him and his new friends to put a end to Celestia's mad ambitions before they can be realized. But the Doctor is no stranger to conflict, and Equestria will learn exactly why he is known as the Oncoming Storm...

*An Alternate Universe story and crossover with Doctor Who for the Negotations-Verse series. Originally posted in Choice, it was decided to make it its own story after suggestions from readers as well as discussions between me and zelkova48.

Please help out at the Negotations-Verse TV Tropes Page: https://tvtropes.org/pmwiki/pmwiki.php/Fanfic/TheNegotiationsVerse