Several months have past since Doctor Whooves entered Equestria and found himself unable to leave, he had wondered how the universe he knew was going to get by without him and on the first year anniversary of his appearance he'll get his answer. Now he must make the choice to either stay with his new friends or return to his old ones. Either way this will decide the fate of the new Time Lord chosen to take his place in either universe depending on his choice. Paging Doctor Whooves, The Seeker is here to see you.
A MLP/Doctor Who Crossover with my Original Character designed from the concept of the Doctor Whooves theory. (The amount of main character's listed will fluctuate depending on their importance in the story at the latest chapter published so... I hope that's acceptable.)

This story is a sequel to The Whooves Collection Episode Two: Vengeful Hate

Twilight has fallen through the time vortex and has been transported back to the Crystal Empire under the reign of the malicious King Sombra. The Doctor comes to her aid, but finds that the Empire holds a dark secret. With the help of a mysterious stallion and his numbers, the Doctor and Twilight face off against Sombra and one of the universe's deadliest foes: the Vashta Nerada.

Episode Written by: Perceptive Key
Cover art is my own, but will be elaborated upon and improved.

Ponyville-1002 C.E.
Twilight begins to learn how to become a Master Unicorn. Then, in the midst of reading, a strange blue box appears, along with a stallion who calls himself the Doctor. Twilight stops him just as he is about to go, but the doors shut and the TARDIS disappears.
.....
Canterlot-297 C.E.
Celestia prepares for the Summer Sun Celebration, but something else has other plans.

Episode Written by: Perceptive Key
Cover art is my own, but will be elaborated upon and improved.

The Elements of Harmony are six of the closest friends in all of Equestria. But when a sudden tragedy strikes down one of the elements, how will the other five be able to handle their lives? Will they find the strength in themselves and each other, or will their inability to cope cause more tragedy for the group?

Featured on Equestria Daily December 30th, 2011

This story is a sequel to A Stitch in Time

Having discovered the message left for her by Star Swirl the Bearded in the distant past, Twilight once again finds herself caught up in the middle of a struggle against forces far greater than herself. In order to even stand a chance she'll need to travel further and wider than she ever has, and forge some unlikely alliances with old enemies. All to bring down the powers that have manipulated and shaped her entire life, and retake control of her own future.

The conclusion of the Time Loop Trilogy, which began with Hard Reset
Available in Spanish thanks to dgs1993
Series TV Tropes page

Twilight isn't having a very good day. An experimental spell blew up in her face, an army of changelings is attacking Canterlot, and she just died. Yet somehow, it looks like it's going to keep going downhill from here.

Given the chance to correct what's gone wrong, Twilight swears she's going to fix all this even if it kills her. Which it will. Frequently.

Cover art by Pixel Prism
Spanish Translation
Series TV Tropes page

Everything in the current Equestria is all because Rainbow Dash performed a Sonic Rainboom. But what if she didn't. If, for some reason, there was no race. There was no Sonic Rainboom. What then?

This story focuses on, what I believe, is what would happen to Twilight under those circumstances, and hence is headcanon.

It all started, or ended really, about two months ago. They came in the night, an unrelenting force that wanted nothing but to watch us suffer.

They took everything from us, including those close to our hearts. Now those same ponies are trying to destroy the very things they wanted to protect. What little we have left, we protect with our lives.

I had one thing left, but now... she's gone.

A storm of epic proportions sweeps over Equestria, leaving the ponies of Ponyville to try to piece their lives back together.

One year after her coronation, Princess Twilight Sparkle is dead, killed by her own subjects out of fear and jealously. After the funeral, Princess Celestia isolated herself from the world, mourning the loss of her brightest student and daughter figure.

But she cannot weep forever. She must take control of her duties once more. Haunted by the memories of the assassination, and its aftermath, Celestia slowly makes her way to Twilight's resting place to find some closure.

Now With its own TV Tropes Page!

Sequel is up