The Doctor and his new companions arrive on the Carrier 9 viral research vessel, quickly finding that it is infested with a deadly plague that eats away at several parts of the body, with only one pony having the means to hold it back. As his companions contract the disease, The Doctor discovers what the pony has been keeping from his patients. But this disease may kill them first.

Derpy has been arrested by R.I.F.T. under the assumption that she knows more than she's letting on. She soon discovers that Lyra is not quite as sane as she seems, and an invisible ally attempts to contact her. But can Derpy really trust her? Meanwhile the TARDIS crash-lands in Fillydelphia, 987, and Pinkie decides a party is needed, despite the giant doomsday device.

Sorry for the horrible parody title. Doctor Whooves and Pinkie Pie! What strange antics shall happen?...

Puzzlehunt and Trixie are captured and end up in the tribe of ponies who are kidnapping unicorns. And sure enough, The Doctor is there too. He meets the leader of the tribe, who is somebody he already knows. The tribe is preparing for the return of the god they worship, and he will consume the planet when he comes. The Doctor is to be sacrificed and his friends will be converted.

An incident in the TARDIS causes the Doctor to once again, get stranded in a parallel But instead of just another parallel earth, he finds himself in the world of Equestria. And while he tries to get his head around the concept of magic, and Twilight Sparkle tries to understand the TARDIS, an old enemy will rise inside the magical kingdom. One that threatens all of Equestria.

What happens if, through a small string of events, The Doctor's personality winds up in a pony? This story is a mixture between Doctor Whooves and my friend akaInYOFACE's story titled "A Twist in Fate 2: Split Screen". Rated M for future language usage, and possibly more in later chapters. Contains Main Six, the Princesses, plus many others from the MLP FIM world.

The Doctor and co. are in the middle of a trip on an airship when pirates attempt to raid them. It isn't long before things begin to seem hopeless, and with the TARDIS so far below on the ground, they have no way of escape...until somepony below manages to turn the tides of the battle around completely. Based on askclockwisewhooves on tumblr.

Derpy is a lonely mare with no friends. Dr. Whooves is a lonely stallion who has left or outlived all his friends. They are perfect for each other. Unfortunately the doctor has something of use for a sadistic factory owner and gets kidnapped. Determined to find him, she sets out on a quest to find him, with the help of a few unlikely ponies along the way.

The Doctor has a quick trip to Equestria and it wasn't exactly a good idea leaving the TARDIS next to that tree house..

The discorded doctor has come to get revenge on the doctor and eon so he can rule the multy-verse and to use a new weapon of times past to become invincible. now heros of different times have come together to stop him. The doctor and eon are running out of time. can they and there old friend s save derpy or will she be stuck as the discorded doctors slave forever?

I hate this world. I don't know how I got here and how to get the heck out. I'm between a rock and a hard place. And if there's a way out of here and I figure it out ill leave in a heartbeat. But... Just maybe... Maybe there is a reason I survived.

Jack and the Doctor are meant to be together. But when the Doctor goes missing, and their relationship is put to the test, will all be lost? Or will they pull through?

The time travelers receive a distress call from the future, leading them to a desert planet. There they encounter a search team that's investigating the wreck of the largest ship in the universe. And they're receiving the same distress call that's emitting from the bridge of the ship. They enter the wreck to find the source of the signal, but find that it holds many more secrets.

On an Equestrian colony 1000 years in the future metallic eggs rain down from the sky as the Doctor discovers some of Pinkies more unusual abilities, also known as Pinkie sense. Meanwhile Derpy Hooves discovers that things in Equestria are not as safe as they seem, and the only pony who knows anything about it refuses to tell her anything.

Daring Do prepares to depart the TARDIS, but the farewell will have to wait, as the Cybermen force them to crash land near Canterlot in 1003. The Cybermen are forcing he Doctor to lead them to a power source powerful enough to open the gates to Tatarus, where the most evil creatures ever are held prisoner in a Nether-dimension. One of which is happens to be the Cyber-Controller.

Upon returning to Ponyville, the Doctor learns that there's a new mare in town by the name of Colgate and that she desperately needs his help. When a chance encounter leads to Twilight and Pinkie Pie getting trapped in the past, the Doctor will have to solve the mystery behind Colgate's curse as well as learn her connection to an ancient and lonely creature.

Part 3 of a longer arc of short stories, partly inspired by Andrew Joshua Talon's "Vale Decem Equis". The Doctor takes a pegasus, a unicorn and an earth pony to where no mare has gone before... but they'll learn trouble always find the Doctor, no matter where he goes.

A horrible short story that's selling point is it shouldn't exist.

Ditzy Doo and the Doctor meet and travel together. But Ditzy isn't who she thinks she is, and the Doctor has a hopeful hunch at who she really is. Is he correct?

What was once Equestria is now in turmoil. An environmental disaster has made severely contrasting climates all over the place, with all of the ones there trying to reach the most hospitable of them, but also the smallest. The Doctor also finds that some one is organizing the systematic assassination and eventual destruction of the whole complex, and he will be trapped inside.

A Doctor Whooves version of ponyphonic's beautiful "Lullaby for a Princess". The Doctor is mourning the loss of his kind, even though he knows he had to seal them in a time lock in order to prevent them from tearing the universe apart.

The Doctor's past selves suddenly find themselves all meeting each other. And the past selves are in for a shock when they see the newest Doctor and his two companions.

After attending a crazy wedding, Derpy asks the Doctor to take her somewhere relaxing. However, their plans are changed when a unicorn by the name of Twilight Sparkle stumbles into the TARDIS and the TARDIS takes them to a war-torn planet over 600 years in the future. Things only get worse when the three travelers are taken prisoner, but this is only just the beginning.

New Gallifrey, A bright and shining world on the 1st Star system of the Universe. It's mission; Interference. If the original Time Lords don't interfere, these do. With their best men on the Job: The Doctor, The Master, Orion and Omega, Jack and Monk. Now, their mission, Stop Vale Yard from destroying the new heritage of Gallifrey. And the Clock is Ticking...

The Master wants to turn Equestria into a giant black hole, It's up to Doctor Whooves and a certain pink mare to save the day. Twilight Sparkle as alicorn, set just before equestria girls. PLEASE READ AND REVIEW!