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Allons-y!

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Beginnings are tricky things. Every effect must have had its cause, and that cause must have been caused by something else, which had something else cause it.

But not necessarily in that order.

The perception of time possessed by most people— and, for that matter, most ponies, dragons, griffons, and other sundry life forms with enough intelligence to observe it— is that time is a straightforward, linear path. Lifeforms fortunate enough to actually experience it, on the other hand, generally arrive at the conclusion that time is rather more like gelatin. “Exactly like gelatin,” they proclaim enthusiastically, “because, you see, it’s…”

“Well, that is to say, it’s…”

“I mean…”

It is at this point that the lifeform in question will begin to search around for the nearest available intoxicant. This unusual routine is rooted in one very simple problem; namely, the fact that time is almost, but not entirely, exactly unlike gelatin. The two have only three qualities in common. They are as follows.

-They are both wibbly-wobbly (note, however, that gelatin is not also timey-wimey)

-Their structures are both virtually incomparable to any other known substance.

-It is probably best to avoid thinking about either of them too hard.

This is the story of one individual (or two, or ten, eleven, or thirteen; it gets rather tricky) who knows rather a great deal about time. (Certainly, they know enough to avoid the gelatin metaphor unless both the explainer and the explain-ee are thoroughly, utterly, disgustingly drunk, such as when one has consumed several banana daiquiris or half of a Pan-Galactic Gargle Blaster) Their name? The Doctor.

Well, alright, that’s not really their name, but let’s not get into that here. You can find it on the Internet, if you try hard enough. At any rate, our story opens appropriately enough. It begins with a box.

Trottingham, Summer 996 CE: A wooden box, it’s blue exterior many shades deeper than the robin’s-egg sky, hurled downwards from the heavens. It impacted the ground, sand and dust sent flying out of the way. A door swung open, and a short and shabby bat-pony stallion trotted out, muttering angrily to himself, “Shoddy CIA aim, typical of them. I mean, REALLY, if they intend to send me around the universe all willy-nilly, I should expect some degree of comfort and—”

He stumbled rather badly, falling flat on his wrinkly face. He pushed himself up, shaking off the dirt, and glanced at his hooves. Then, with a start, he stared down at them. He felt at his muzzle, his mane, his wings. “Oh my giddy aunt,” he breathed. “Jamie, get out here!”

Canterlot, Spring of 875 CE: The banging of hoof against wood echoed through the halls of the Equestrian Intelligence Agency. “Go away!” a reedy, petulant voice replied.
Commander Rapid Rounds groaned inwardly. “What in Celestia’s name did I do to deserve this?” he grumbled. In a louder voice, he said, “Doctor Tempus Fugit, you can’t sulk in there forever! Come out, and let’s discuss this like gentlecolts.”
“Who’s sulking?” the EQUIA scientific advisor asked. “I am merely trying to figure out how to get out of this benighted universe and return home!”
The captain rolled his eyes. Ever since the Doctor had arrived, they’d proved to be nothing but trouble and misery, grousing about how they’d very nearly repaired their TARDIS just before it blew a fuse, sending them through the dimensional rift to ‘another bloody army base, I swear this body attracts them’ as they themself put it.
Still. There was, he had learned, ONE way to get them to behave somewhat rationally. He turned away from the door, adding casually, “Ah, well. If you’re as busy as all that, I suppose we can get someone else to look into these unexplained deaths…”
The door flew open, a ruby-coated crystal pony practically springing out, shock of white mane frizzed wildly. “WHAT unexplained deaths?”
Commander Rapid smirked inwardly before hoofing the Doctor the dossier.

Unicornia, Winter, Pre-Unification Era: Starswirl the Bearded was not easily nonplussed. The stallion had faced indescribable tentacled horrors, maddened and maniacal sorcerers, and Princess Platinum on a bad mane day. It rather said something, therefore, about the state of the current courtiers when even the great Starswirl was struck dumb by the recent turn of events. The mysterious blue box sitting in the center of the room was befuddling enough, but then a pair of earth ponies had stepped out— an unusual occurrence even before taking into account the fact that the box was too small to hold them. It was difficult to say which of the two was more disconcerting. The female, a red-maned yellow mare, seemed almost at home here in the opulent court of Unicornia. Her eyes were the only thing that betrayed her, darting hither and thither at the very confused armed guards surrounding them. It was the stallion, however, upon whom everypony’s attention was fixed. He had… gravitas, the wizard decided, this stallion with the wild eyes, the curly mane, and the trailing and multicolored scarf around his neck. Suddenly, the fascinatingly peculiar stallion spoke. “I say,” he murmured in a low baritone, his icy blue eyes darting about the chamber, “it’s rather chilly in here, isn’t it?”
Turning to the mare, he continued, “Apple Core, wouldn’t you say it’s rather chilly in here?”
“You’re one to complain, with that scarf off yours,” she returned, her vigil against the guards never ceasing.
“Hm.”
Suddenly, he turned to the princess, the highest-ranking official in the land, notoriously classist and snobbish, and asked without preamble, “Excuse me, but would you care for a jelly baby?”

An earth pony village, Summer, Pre-Unification Era: The two young mares stared cautiously at the blue-coated stallion standing in front of them.
“How do you know our names?” demanded the white-coated one.
The stallion simply smiled enigmatically. “I’ve met you both before, little Celestia. But I rrratherrrr believe that you might not rrrememberrr that just yet.”
He leaned forward against his umbrella, piercing grey-blue eyes boring through them. “Trrrust me,” he burred. “I’m a Doctorrrr.”

Ponyville, Fall of 997 Celestial Era: It had been five years ago when they had first met, the grey pegasus with the crossed golden eyes and the kind, absentminded purple unicorn. They had met at a party. He had walked up to her, nursing her cocktail in a corner, looked straight into her crooked eyes and said with absolute sincerity, “Hello, you look quite beautiful. May I kiss you, or would that be too forward?” She decided that it probably would, but they had danced all through the evening, nevertheless.
They had met against the next week. He had listened to her shimmering laugh and said, “Wonderful.” They had kissed.
This had kept up for several months. Then, one day, he had gotten down and pulled out a ring. He whispered, “Please.” She had smiled and whispered back one word. The smile on his face threatened to split him in two.
Months later, on their wedding day, he had looked deep into those wandering golden eyes with which he had fallen in love and whispered, “I do.”
One year later, he had looked down at the newborn filly in his hooves, with her father’s coat and her mother’s mane and, crying, whispered, “Perfect.”

But there is no such thing as perfect. He had become worried and distant. At night, he would stare up at the stars, as if trying to remember something… or perhaps trying to decide. He could feel the war in his bones, even from this far away. He felt time beginning to fail, felt his species dying out, felt his home falling. And so, he looked into both sets of golden eyes once more, those eyes for whom he would do anything. And then the Doctor whispered, “Good-bye.”
And he was gone.

London, Winter of 2005 A.D.: The Doctor pulled a lever, vanishing away from his last glimpse of Rose Tyler. He breathed heavily, his hearts skipping erratically, his body beginning to burn. As the TARDIS hurtled through the Vortex, he rasped with his final breaths, “I don’t want to go.”
But, in a burst of golden flame, he went anyway.

Here and Now: But where did he go?
Practically every bipedal culture has developed some iteration of the famed Trousers of Time. Ponies did not discover this, though minotaurs did. This is the quantum bifurcation of timelines into separate and distinct ‘legs’ whenever a choice is made. E.g., the cat is either alive or dead, the Doctor either regenerates or dies, the prize inside is either a wicked cool disc shooter or a lame-o top. The only way to find out which one happened is to open the box. Once the notion of the Trousers is developed, the clever person that invented it is generally quite satisfied with a day’s hard work done and goes down to the pub to boast about it over a pint of bitters. This usually precludes them from remembering something rather important about trousers. Namely, the fact that, when under sufficient strain, they will rip. A flaming, out-of-control TARDIS is rather a great deal of strain indeed.
So it was that the fabric of spacetime wibbled. It wobbled. And then, in a moment of flaming glory, it rent itself in twain for just one fraction of a second. In Ponyville, an elegant white unicorn suddenly felt the need to go take a cold shower.