This story is a sequel to The Doctor Whooves Chronicles Episode 3: The Monster in the Mirror

For their first willing trip together, the Doctor and Derpy find themselves in the underwater metropolis of Atlantis. However, the saltwater utopia is burdened by terrorists who wish to keep Atlantis separated from the overworld. With the Prince of Equestria visiting and the life of the King of Atlantis threatened, the watery city is about to reach its boiling point.

This story is a sequel to Doctor Whooves Episode 15: The Christmas Ponies

The Doctor, Twilight, and Derpy decide to take Donna to Equestria. However, they accidentally end up in the year 56, where Equestria is currently caught in a bloody war with the newly-founded Changeling Empire. When Derpy and Donna are taken captive, the Doctor and Twilight must team up with a hardened Celestia and a simple farmmare in order to stop the merciless Queen Esmeralda.

This story is a sequel to Doctor Whooves Episode 16: A Country at War

The Equestrian and changeling armies have suffered greatly from the battle. Esmeralda is ready to end the war once and for all and sets her sights on the last safe haven in Equestria: Canterlot. As Donna ventures into the Changeling Castle to find Esmeralda's greatest weakness; the Doctor, Twilight, and Angie take charge and Angie goes beyond what she ever expected of herself.

This story is a sequel to Doctor Whooves Episode 17: Angie the Great

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.

This story is a sequel to The Wandering Physicist Adventures

Seven years after the wedding on Twilight Sparkle and James Wanderer, life in Ponyville is pretty normal.

Apple Bloom runs the library for Twilight Sparkle. Applejack and her son have a happy family life. Sweetie Belle attends music school in Canterlot, living with her sister in Rarity's new shop. Scootaloo works full-time for Rei, who is finally married to Inkie, while training to join Rainbow Dash as a Wonderbolt. Fluttershy and Sunshine raise two lovely foals of their own. Pinkie and the Cake twins work to make everypony in town happy. Trixie, Stormy and their daughter travel the world performing. Just normal life for everypony.

One day, The Master shows up in Ponyville to torment his old 'friend', The Wandering Physicist. Instead, he ends up harassing everypony TWP cares for as a distraction while he tries to conquer Equestria. Everypony will have to keep their wits about them to survive the threat of the deranged Time Lord and prevent him from destroying the land they love.

Sequel to The Wandering Physicist Adventures - Written in a manner so that all necessary backstory is covered within. No real need to read TWP, but it is appreciated.
Prequel to Starlight Chronicles

Character References: On tumblr - On Deviant Art - Warning: Contains spoilers and peanut products.

The Doctor and his companion Darkfire go on a trip to Zenchon, but a rift opens, pulling them in. They meet 3 other Doctors and their companions. Now, they must stop the evil Destructo who is keeping them in this Alternate reality, and return home.
Trailer: http://www.fimfiction.net/blog/157654/time-pony-trailer

Derpy has always been the sad kind of pony. Her completely unfocused eyes haven't helped at all. She had been teased all her life and was just at the brink of ending it all. No more sadness, no more mockery. That's when she met an interesting stallion who changed her life for the better.

The left wall of Sugarcube corner had been nearly completely demolished by the box, and it was a testament to the skill of the earth-ponies who had constructed the building that it was still standing at all. She shook her head and went to examine the words at the top of the thing that had caused all the havoc.
"Police public call box" she murmured softly, eyes almost glowing with curiosity

Twilight Sparkle is planning on having a relaxing day, but that all changes when a blue police box crashes into Sugarcube corner. Now Twilight, Pinkie, and a strange stallion named the Doctor have to try to save Equestria from a threat disguised as their own beloved ruler.

Currently going through a chapter by chapter rewrite, so apologies for any disconnect between edited and unedited chapters
Chapters currently rewritten:
Chapter One
Chapter Two
Chapter Three

(Sequel to Doctor Whoof: Time of the Hourglass)
The Doctor, after a tiring week trying to repair the TARDIS again, has decided that he needs a little vacation. After hearing that Apple Bloom is heading to Appleloosa to visit her cousin, he volunteers to accompany her. However, things arnt as peaceful in the small town as The Doctor had hoped.

Can The Doctor and Apple Bloom fight off the metal menace of the Cybermen, in pony form? How did the cyborgs get to Equestria in the first place? And will Braeburn ever fix that yelling problem he has? Find out in the third enstalment of Doctor Whoof! (Cyberpony art found on Google)
(Start from the begining with Doctor Whoof: Day of Discord )
(Continue to read the epic adventures of The Doctor in Equestria in Doctor Whoof: Battle Royal )

(Sequel to Doctor Whoof: The Iron Horse)
The Doctor has faced two of the challenges that Zecora prophesied, and he is dreading the third. On one hand...um, hoof... the time colt wants to return home, on the other he knows he will miss his friends dearly. However, this is put on hold when Twilight asks the strange brown colt to root for her at a tournament in Canterlot.

Around the same time, Rarity has to go to Canterlot to pick up a dress. Is this the final trial for The Doctor in Equestria? Or is this the final trial... of his life? And is Rarity truly going to Canterlot to get a dress, or are her intentions cloaked in darkness? Find out in the fourth entailment of Doctor Whoof! (Art found on Google)
(Start from the beginning with Doctor Whoof: Day of Discord. )