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 1: The Doctor in the Box

Following an accident with the TARDIS, the Doctor and Twilight find themselves 1000 years in the future. Here they find a futuristic Equestria, a confused Queen Celestia, and a pony from the Doctor and Twilight's future who wants revenge.

Flash Sentry has come to accept that in a world now full of magic, someone like him is nothing more than a side character despite how much they want to help. He's sent to live a life of boring mediocrity, until one unexpectedly strange day. From out of nowhere, a pod comes crashing down to earth. And inside is a device that will change Flash's life forever. The Omnitrix.

Written with the help of SuperSonicHeroes

Art by SlidDiamond3214

TVTropes

(The epic cover art was drawn by Mutter Butter! Thanks to them!
https://www.fimfiction.net/user/297066/Mutter_Butter)

Eons ago, in the trades of Nekravol, the great Khan Maykr sold away large stocks of worlds and planets that were once under their jurisdiction to the Dark Lord of Hell. Amongst these worlds being the peaceful land of Equestria. The Dark Lord saw the powerful magic that inhabited this equine ruled land and decided that rather to invade immediately, it would be wiser to save it in an emergency where he was no longer in power.

Equestria, a land where almost nopony experiences grievances, pain or agony. Literal sunshine and rainbows. However with new revelations about this world, it's inhabitants may experience a drastic shift in their hopeful home.

Ever since a weird red substance was discovered by Applebloom, peculiar things have been occuring around Ponyville. Frightful creatures, odd diseases and strange events. All much more frequent than usual. Could this amount to something much more substantial for our equine friends?

(Supposed to happen between the end of Season 6 and the start of Season 7 and after the end of The Ancient Gods 2, the last DLC of DOOM Eternal. If you are here for the action, Cordial Affairs and all the Mission chapters might be what you are looking for.)

Pinkie Pie is being tormented by horrific nightmares. Unable to deal with it by herself anymore she seeks out Twilight's help, but will it have been the best decision when she finds herself alone in an abandoned, fog filled Ponyville?

Sequel: http://www.fimfiction.net/story/4676/Too-Shy-for-a-Rainbow

There have been a LOT of high-quality readings of Silent Ponyville, but this one is my personal favorite:
https://www.youtube.com/playlist?list=PLGh01rbB4o3xoSV7a6Omc-UJROXHRZ1Hv

After the Friendship games, the Mane 7 sets out to camp Everfree to solve some hidden secrets with the living entity Gaea Everfree. But they will be met by another evil not from equestria but from hell.

The 1971 Lincoln Continental Mark 3, named Trinity is about to come across the Mane 7 in a non hostile way, but to solve the mystery of Gaea Everfree and save the camp from the imminent foreclosure, before it's too late. But a battle between a Forest spirit and a motorized monster is about to begin.

And there were many questions.
Is it a phantom, a demon, or the devil himself?
What Evil Force Drives....... THE CAR?

Note: I do not own any of the movies it is just a idea to make a crossover
Equetria girls belongs to Hasbro
THE CAR belongs to Universal

This story is a sequel to Doctor Whooves: Only My Will

Cover art by: _Vidz_

Edited by: Ephraim Blue

The Doctor has regenerated, a new face, a new attitude, and of course, new troubles.

Ponyville seems to have survived the ordeal, but the Doctor has arrived again with a few new questions.

What will this new persona mean for the Doctor's future?

What is the significance of these two musicians that he has been led to?

Who exactly is "Blue," and how does he know the Doctor?

And finally...

"What do you want?"

This story is a sequel to Doctor Whooves: Silence Will Fall

The Lynchpin Quintet Part 5 of 5.

The Doctor has been called back to present day Ponyville, and it's in ruins. The Black Guardian has provided the Master with an army of his deadliest enemies. The Master has kidnapped Applejack's friends. All in a relentless search for one thing. The final Lynchpin of the Multiverse. The Key to Time.

The Doctor knows what will happen if the Master gets his hands on it. A doomsday that will make not only this universe, but all others, perish in flames.

He knows something else as well.

His time is coming to a close.

Edited By: Ephraim Blue

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

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