The Doctor and his companions return to 1002 and arrive in the middle of Canterlot. Meanwhile, a Dalek appears and names Princess Luna as its next target.

The Doctor heeds Applejack's request and has the TARDIS take them to July 6, 996, a day that changed Applejack's life forever.

After a month of traveling, things seem to be going well for the Doctor and his companions. However, after a certain egotistical unicorn appears in the TARDIS, they find themselves trapped in an army base that has a bad infestation.

The Doctor and his companions arrive in the Griffin Kingdom in 1021. Here they come across a future Rainbow Dash as well as a killer from an alternate dimension with a familiar face.

The Doctor, Twilight, Derpy, and the others arrive on a luxury spaceship in 4376 and soon find that there are some unwanted guests on board.

With Thalia growing closer to destroying Ponyville, it'll take two Doctors and the return of an old ally to stop them. A new chapter in the Doctor's adventures in Equestria is about to begin.

The Doctor and Twilight finally return to 1002 only to discover that they've arrived a little bit late. Meanwhile, an old enemy returns to take their revenge on Ponyville.

The Doctor and Twilight, after accidentally picking up a mysterious mare named Matilda, end up 100 years prior to the birth of Princess Celestia and run into the king of chaos himself at a time when he was actually good.

The Doctor and Twilight end up in Canterlot in 987, where they come across a young Shining Armor and a devious villain who has dark plans for the young unicorn.

The Doctor and Twilight find themselves 1000 years in the future, where a deadly enemy waits for them.

The Doctor and Twilight arrive on the planet of Eugora in 1899 and come across an army base in need of a doctor as well as two enemies that have dark goals in mind.

The Doctor finds himself in Equestria following a violent regeneration and is forced to work alongside an annoyed Twilight Sparkle in order to defeat an old enemy.