This story is a sequel to Doctor Whooves: When Universes Collide

The holidays at Canterlot High are always lovely. Bells ring, children sing, and old friends reunite. Sunset and her friends are in good cheers when the Doctor returns for a visit. However, he discovers a crack in time leading to Equestria. Even when he closes it, the crack returns, and a swarm if Changelings comes out of it. With the TARDIS sent off who knows where, the Doctor is stuck between a rock and a hard place, as he must protect all of Canterlot High's students from the Changeling Invasion.

'Alternate Universe' tag for slight differences in the timeline.

This story is a sequel to Doctor Whooves Episode 22: Black Sun

The end is here. The players are in place. Both the Doctor and Discord Whooves are ready for the endgame. Big changes and great sacrifices await as the war with Discord Whooves reaches its devastating conclusion.

After the Doctor saved the world and got a new companion, Twilight Sparkle, he has been told she is moving. Her mother Twilight Velvet has a request for him. To go to check out the new school Twilight will be attending. But when he gets there he is thrown into a new adventure where he meets a strange Twilight, as well as an energy source in this school. Meeting old friends and helping bring together friends, the Doctor is in for an adventure even he has never done.

The Doctor and his faithful companions, Derpy, Dinky, Lyra, and Bon Bon go to Canterlot to attend the royal wedding of Shining Armor and Princess Cadence. Little does the Doctor know, a dark force waits ready to take everything he holds dear.

The Doctor tells the Watcher the story of how he came to Equestria and why he ended up staying. How will this change the Watcher's view of the Timelord who killed her race?

After the Doctor's adventures in Equestria, the Cybermen and Daleks have returned: Only to have the Cybermen into ponies too! They wreak havoc in Equestria, and it's about time the Mane Six learn the truth about that 'crazy' tied colt who calls himself a Doctor and constantly runs around Equestria. But it's only the beginning and something happens to Doctor Whooves.

Written in celebration of 50 years of Doctor Who!

When the 10th Doctor regenerates, his 11th incarnation is a little different than we all know with looks. Even worse, he has landed in a new (but familiar) world. Now he has a new TARDIS and a new companion, Twilight Sparkle. From Alien Prisoners to Weeping Angels, this Doctor will succeed at it all. Equestria Girls universe, possible Doctor/Twilight. Avante!

A blue box has fallen out of the sky, and crashed right into Twilight's Library! A strange brown stallion, calling himself the Doctor stumbles out. Soon after, strange stone Pegasus are everywhere, one of resident weather ponies has vanished, and Twilight is tossed in the middle! The Doctor and Twilight have to find out what's going on, before it's too late!

This story is a sequel to Doctor Whooves Episode 4: Young Armor

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.

The Doctor suddenly finds himself in the magical land of Equestria and soon discovers that he's regenerated into a pony. As Twilight Sparkle tries to learn more about the Doctor with the help of Spike and Princess Luna, a creature from the Doctor's past arrives in Ponyville with evil intentions.