This story is a sequel to Doctor Whooves: Invasion of Manehattan

Starlight Glimmer has succeeded, she has managed to steal one of the Star Swirl spells from the forbidden section of the Canterlot library and, after months of work studying countless tomes of arcane magic related to time, she will be able to defeat that princess of friendship and her friends before even meeting her.

All she has to do is stop the brat that was Rainbow Dash from doing the Sonic Rainboom on her. But before she does, somepony stops her and asks her a simple question, 'are you sure you want to do that?'

"So... Doctor... care to take a stroll in our private garden?"
On the run from Gallifrey, the First Doctor encounters Celestia and Luna in the pre-classical era. And the encounter changes the destinies of all three of them forever.

This story is a sequel to Doctor Whooves: Born Into Darkness

The end of all things. When the universe dies all is meant to be empty of life...

The Doctor knows this, but he can't help but be curious. So he travels to the last star holding out in the void, slowly blinking out as a massive black hole in the centre of what is left of the universe prepares to begin life anew, as it has done so many times before.

But the star isn't alone...

After saving Ponyville from the Cyberponies, the Doctor takes Derpy, Dinky, Vinyl and Octavia on their first adventure through time and space. Their destination; The Splendor, a massive cruise ship travelling the stars and powered by one. But, as usual, it doesn't take long for things to take a turn to the worst as the ship is overtaken by some hostile invaders with very nasty plans for the most amazing cruise ship in the galaxy. The Doctor must save not only his friends and the guests of the ship, but an entire world. The balance of an intergalactic war is on the line, and only the Doctor can save everyone.

No pressure.

The Doctor, a Time Pony, leaves his home-world, Gallopfrey, because, quote, "It's really quite rubbish." He finds a world called Equestria, which is more than a bit strange. For one thing, it's a geocentric system rather than a heliocentric one. He decides to investigate, but finds his query cut short by a visit from some old foes, the Cyberponies. Joined by the wall-eyed Derpy, the psychedelic songstress Vinyl and the refined Octavia, the Doctor must find a way to save his new friends and all of Equestria.

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.

Most ponies, when they see a pony with an hourglass cutie mark, would figure that it would mean their talent has something to do with time, or clocks, or another harmless meaning. Technically, the first is true, but there is a hidden meaning beneath it. To those that carry it, they know that the hourglass marks them as refugees, survivors from a war that would make any normal pony go mad from glimpsing just a fraction of the sheer scope of it. These unusual ponies have all found asylum in Equestria, but now, one last escapee will be followed by an evil that will threaten to ignite the conflict anew and bring down their last refuge with it.

But this newcomer not only brings the remains of the conflict with him, but is their best and only hope of ending it once and for all.

The last gasp of the Time War has come to Equestria. The Doctor will find old friends, make new ones...and face off with one of his greatest foes, one last time.

The Sequel to Number 12.
The Doctor and Twilight leap into the future, though it may be a far darker place than they envision. In the mean time somehow the Doctor keeps crashing around Ponyville, something to do with Fluttershy, but what?

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!

Hearth's Warming has always been a time for family and friends. A time when the ponies of Equis remember the frigid days before the rise of Modern Equestria, and bask in the warmth and comfort of their loved ones.

But for one particular holiday season, strange things are happening in Ponyville that can’t be easily explained. Least of all by Scootaloo, who is having her own share of troubles during this normally festive time of year.

When the mirth and whimsy of Hearth’s Warming starts to take on a more dour and icy edge, things take a turn for the stranger when out of the blue, the enigmatic “Doctor Clockwork” appears.

Join the Hourglass Stallion as he takes it upon himself, his temporary companion Spike, and the newly-conscripted Scootaloo to save Hearth’s Warming before the holidays are ruined forever!