This story is a sequel to Doctor Whooves 3: The End of the Universe

While it's only been five months for Twilight, but for The Doctor, it's been two years. Now he's returned to Equestria and is back as the 10th Doctor, and Twilight is very glad to see him. Looking for a break from her royal duties, The Doctor takes Twilight to where he comes from, which just happens to land at Canterlot High. But, the vacation is cancelled when a student is dead with a strange virus of Zygon origin. With the help of Sunset Shimmer, The Doctor and Twilight must save all mankind from the fatal Zygon disease.

This story is a sequel to Doctor Whooves: The Adventure Continues

When the TARDIS arrives at Canterlot High, it gets trapped in a temporal schism, causing it to bounce between three time periods, 1991, 2015, and 2100. The problem is, The TARDIS has no Doctor, just his companions, and The Doctor is trapped in 1991, with no way to communicate with Twilight and Sunset. In order to communicate through the years, The Doctor must put his fate in Canterlot Highs newly appointed principals, Celestia and Luna, to save the TARDIS from falling into the void.

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: The Temporal Schism

With Earth now combined with Equestria, everyone is switching between being humans, and being ponies. When Twilight tries to get Ponyville under control, she discovers that Equestria has a Doctor of it's own, and that he's one of the few people who can help. Once the real Doctor escapes the clutches of Omega, he returns to Canterlot High to discover what has happened to the world. With the help of his copy, The Doctor must stop Omega, before Earth collapses on itself.

This story is a sequel to Doctor Whooves

After Rose decides to stay in Ponyville for a little while, The Doctor takes Twilight 1300 years into the past, so Twilight can meet her idol, Star Swirl the Bearded. But, fun turns to panic when The Doctor finds out there might be a Weeping Angel in a cavern. With the help of Star Swirl, The Doctor, and Twilight must destroy the Weeping Angel, before Discord arrives.

With the TARDIS in an unknown location, the Doctor has become a pony in Equestria. After finding Rose, enemies from his world appear and begin to attack Equestria. Without the TARDIS at his disposal, the Doctor, Rose, and a pony named Twilight Sparkle must destroy the Doctor's enemies, before they destroy Equestria.

This story is a sequel to Doctor Whooves 2

After returning to Ponyville with Twilight, The Doctor has a vision about something strange in the Crystal Empire, and takes Rose and Twilight there to investigate. But during his investigation, he finds out that he wasn't the only Time-Lord to survive the Time War. When the Crystal Empire is turned upside down, The Doctor, Rose, Twilight and Princess Cadance, must face the Doctor's worst enemy. Who seems to know about The Doctor's future.