Twilight and the Doctor end up in Ponyville, 1026 C.E. during Nightmare Night, but the playful scares soon turns serious as ponies are mysteriously found burned, scarred, and colorless. The only clues are sightings of a cloaked figure roaming the streets that night. There, they meet up with 43 year old Twilight Sparkle, who might not even know what's going on, herself!

The Doctor and his new friends face off against Diamond Dogs and the troll-like Grundels in a race against time to prevent the release of an ancient evil.

After witnessing a series of strange events Twilight Sparkle and friends search for answers, only to find themselves entangled in a war between two ancient races and a plot that could end all existence. Luckily, our heroes find help in the form of an eccentric brown pony with an impossible blue box.

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.

The Doctor of the pony universe lands in Equestria. He meets new friends and battles old enemies. The Fate of Equestria is in his Hooves. Starring: Doctor Whooves; Derpy; Dinky; Vinyl Scratch; and Octavia.

The Doctor, Twilight, Derpy, and the others return to 1002 and arrive right in the middle of Canterlot a mere five minutes after their original departure. They arrive to find a troubled pair of alicorn sisters and an eccentric stallion who knows the Doctor well. However, they also come across a Dalek who has named Princess Luna as its next target.

A regular pegasus is whisked away on an amazing journey through time and space.

The Doctor and Twilight return to present day Equestria for the annual Winter Wrap Up. But some old enemies of the Doctor's have evil plans...

The Doctor heeds to Applejack's request and has the TARDIS take them to July 6, 996. It quickly becomes apparent that Applejack has a plan to change a certain event that occurred on this day. But her choice to attempt to change her future could very well lead to the destruction of the entire universe.

One day Discord Whooves (aka the anti Doctor) finds that a strange Pegasus has entered the TARDIS, and she is intent on staying no matter what he says. Follow the story of Star Gaze and her adventures on the TARDIS with the Doctor and Captain Jack Harkness. See how this young filly deals with the two boys on the TARDIS, and everything else she may find. *Rated T to be safe*

When his oldest enemy returns to threaten the universe again, the Doctor will return to defend it. Can he still save the day, even when his mind is falling apart? Ditzy thinks so. She trusts him even when he doesn't trust himself. How could she not?

The Doctor comes back to Canterlot for a wedding. Only the wedding isn't what the Doctor expected it to be! Based on MLP: FiM: A Canterlot Wedding. Contains spoilers. Also features Kanade and Yuzuru from Angel Beats!

It's been a month since the Mane 6, Derpy, and Spike started traveling with the Doctor. Things suddenly take a turn for the worse when a foil from Twilight's past mysteriously appears in the TARDIS and they all end up trapped in a seemingly-abandoned asteroid base that has a bad infestation.

You've seen the elements of harmony in action, the six bearers being best friends, and the ponies that have been the focus of My Little Pony for a whole two seasons. But what do the ponies seen in the background do during the adventures of the mane six? Read here about six ponies with conflicting personalities as they try to become friends and go on amazing adventures.

The Doctor, Ditzy, Sparkler, and Dinky decide to go visit Raggedy, and wind up in London. How? I'll explain later. The Doctor is his 12th self, having regenerated before ever going to the MLP universe. I wonder how Ditzy and the girls will react to being in a different dimension with seemingly no way back? Only one way to find out!

The TARDIS brings the Doctor, Twilight, Derpy, and the others to the Griffin Kingdom in the year 1021. Here they meet a 38-year-old Rainbow Dash training for the Gailenean 1000. Meanwhile, a third Rainbow Dash from an alternate reality appears but with much darker goals in mind.

The Doctor, the Mane 6, Derpy, and Spike travel to 4376 and find themselves on a luxury spaceship called the Queen Philippine, which is currently on its maiden voyage. What starts off as an interesting adventure turns into a fight for survival when the ship loses power and becomes host to some unwanted passengers.

With Thalia continuing her invasion of Ponyville, Derpy and the others find their last chance at stopping her in the hooves of a future regeneration of the Doctor. Meanwhile, the Doctor teams up with an ally from the past to rescue Twilight and Rainbow Dash and ultimately save the town.

Can the doctor repair the TARDIS and get off this planet filled with talking horses?

When a flash of light envelopes Ponyville chaos ensues. Only a handful become immune in a new world where they are almost non-existant and cannot interact with anyone but themselves. The Doctor gives a hoof, but must do something before an ages old menace decides to envelop Equestria with its hungry vengeance...

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.

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.

A Doctor Whooves fanfic. Inspired by Lissy-Strata's artwork. The Master has taken on the inexplicably brilliant yet socially awkward Derpy Hooves as an assistant. As much as she annoys him, she is particularly useful. Especially when she accidentally swallows the TCE, giving her hiccups a rather amusing power. Amusing to everypony but the third Doctor, that is.

'Doctor Whooves' and 'Roseluck' aren't who they seem. Indeed, barely anypony really knows who they are or where they came from. All they know is that their arrival was rather sudden. One morning, without warning, there they were ready to join the Ponyville population. There wasn't anything suspicious about it, of course. Many, many ponies come to live in Ponyville rather suddenly.

'Things have changed since ya left wit' him, Twahlaght...' The Doctor and Twilight Sparkle land in a future version of Ponyville to find significant changes in Equestria. Doctor Whooves fic.