This story is a sequel to Doctor Whooves Episode 18: The Mystery of Colgate

Colgate crosses paths with Clockwork and Bright Eyes following her arrival in the tourist-centered, mysterious country of Elmheim. Upon crossing paths with Matilda and a universally-displaced Daring Do, the group sets out into the jungle to discover the hotspot for dimensional rifts in the Equestrian universe. But their trip to the rift epicenter will be far from simple.

Dinky and Sparkler weren't always a part of Ditzy "Derpy" Doo Hooves's family. That much is quite obviousto Ditzy's best friend . Ditzy tells how she came to have two wonderful daughters in her life, all thanks to the Doctor.

Title says it all. Time travelling shenanigans ensue.

The year is 990.
Celestia is sending a beacon of light out into space quite regularly. She's trying to make contact with an old friend of hers. She wants him to take Luna with him. She wants him to break his vow of never returning to the moon.

She calls upon the Doctor.

Art credit goes here: http://ciscoql.deviantart.com/art/Princess-Luna-inside-the-Tardis-with-Dr-Whooves-388629525

Twilight Sparkle was on her way to buy a sapphire cupcake treat for Spike, but she couldn't seem to find the Cakes. As she starts to investigate, she comes upon a dark, dusty corner, where something moved. Curiously, she approached it, when it suddenly lashed out at her. She was saved just in time by a mysterious pony who claims to be "The Doctor".

His cutie mark and blunt speaking only fueled Twilight's curiosity, and it wasn't until it was too late that she discovers what needs to be done to save Equestria.