This story is a sequel to The Three Sisters

What if... After "The Three Sisters" Rarity managed to find Chrysalis and talk to her?

A definite sequel.

Now with a TV Tropes page! Warning: will contain spoilers.

The sequel to Wayward Courier. Read that first, or you'll get lost.

Two months after his first visit to Equestria, Thomas has returned. And this time, he's not alone!
Now the ponies have to deal with not only him, but a depressed snarky ex-Scribe and a Brotherhood Ghoul with her own list of incredible achievements and emotional baggage.
However, things aren't well in Equestria, as they quickly find out...

All major details relating to Season 3 are non-canon to this fic.

Getting a college roommate is random chance.
Sometimes you get lucky, and sometimes you get a pony.

Rainbow Dash enrolls at an Earth university.

Update: and then some other stuff happens.

This is an idea that wouldn't leave my head, inspired by Fairy Slayer's "Mommy Nearest," Aldea Donder's "Alicorn," SoundofRainfall's "Play" and RainbowDoubleDash's "Lunaverse"

Alternate Universe: Instead of Twilight Sparkle, Princess Celestia made Rainbow Dash her personal student instead! Follow her through the events of the 1,000th Summer Sun Celebration. A reimagining of "Friendship is Magic"

Following the events of "Traveler," Twilight goes to Canterlot to deliver her report on what has transpired since the Doctor's arrival in Ponyville directly to Princess Celestia. She leaves the Doctor in Spike's capable claws, asking him to show Equestria's newest arrival around town while the TARDIS rests and repairs itself from the trials of the previous day.

Although at first distraught at being stranded in the seemingly serene township of Ponyville, the Doctor finds himself reexamining his initial assumptions about the ponies, the land of Equestria, and his compulsive need to travel when he is confronted with the miraculous, impossible events surrounding Ponyville's resident party mare: Pinkie Pie.

The Pinkie Conundrum is the first in a series of continuity branching off from the foundations established by the Doctor Whooves stories: Number 12 and Traveler by the very talented Squeak-anon and all references to these two works of fanfiction is credited to him. Also, while this is a separate continuity from any future works by Squeak-anon, it is strongly recommended to read these two fictions before reading Pinkie Conundrum.

This work has been developed and published with permission and blessing of Squeak-anon, my original inspiration.
Doctor Whooves Intro posted on YouTube by: Cshep99
Cover art provided by FoxInShadow from deviantart.com
Proofreader, Editor and Number One Assistant: 2dextreem

If you enjoy this story as well as my other works, please leave a comment. Constructive critique is encouraged as well as any questions or remarks that may occur.

What if Queen Chrysalis won? What plans does the queen of changelings have for the citizens of Canterlot? And what is with the wails of pain and suffering coming from the bedrooms in the castle? Will Twilight avoid a terrible fate or is her own imagination getting to her?

After losing a good friend who will no longer remember him, an incident in the TARDIS causes the Doctor to get stranded in a parallel universe. Instead of just another parallel earth however, he finds himself in the world of Equestria where ponies rule. While the Doctor tries to get his head around the concept of magic, and Twilight sparkle tries to understand the TARDIS, a disaster occurs when the Doctor inadvertently reveals a terrible secret, and an old foe from the Doctor's past will try to take over Equestria. The Doctor and his knew found allies our the only ones who can save the day.

[Tales of the Carnageverse]

A rewrite is coming soon. Please don't read this how it stands, it's bad.

T for Teen. Violence, and Major swearing. Fallout 3 crossover, because it hasn't been done before.