The six mares went on many more adventures with the Doctor. They saw the farthest reaches of the universe, met all kinds of new beings, and fought many foes. For a while, it seemed like one great dream from which they never wanted to wake up.
But soon, their love for home, friends and family caught up with them. As wonderful their adventures had been, they agreed it was time to go home.
They arrived a few weeks after they had last left, and were met with open arms. All of Ponyville had gathered to welcome them home; somehow, Pinkie had been able to tell them of their return.
Each of the six mares had something to show for their journey. Twilight Sparkle's bags were full of new books from other worlds, and her mind was swarming with new research ideas. Rainbow Dash had employed all sorts of new tricks against the monsters they met, and was eager to adapt them into flying tricks. Rarity's cargo, dutifully transported by the stallions of the village, consisted of several large crates of exotic fabric for new dresses. A cartload of seeds and fertilizer made its way to Sweet Apple Acres as part of a bet between the Doctor and Applejack to see if apples from the future tasted as good as hers. Fluttershy had the least of them all; just a small tea set and some flower seeds to give to Carrot Top and Roseluck.
Pinkie's loot was meant specifically for that evening.
The "Say-Goodbye-to-the-Doctor-Party" was especially big, even by Pinkie Pie standards, as to "make up for lost time," as she put it. The entire town was invited, and all night they enjoyed food and song, and gathered around the Doctor to hear his tales of his adventures across time and space.
As was tradition with Pinkie Pie, the party never officially ended. Ponies simply said goodbye when they were tired. Some even managed to stay until morning. After the last guest left, the six mares and the Doctor had their own little party, which consisted of reminiscing over a pot of tea. They talked and laughed and simply enjoyed their friendship, not wanting to end their time together.
Yet on the morning of the third day, they knew normal life had to continue. The weekend was over, and they all had jobs to perform and family to take care of. As much as they hated it, it was time to say goodbye.
"Do you really have to go?" Fluttershy asked.
"Surely you can stay a while longer," Rarity offered. "If it's a matter of money, you could always help in the boutique; I've been meaning to start a line for stallions for a while, and you would make a fabulous model – "
Applejack touched the unicorn's shoulder. "Ah don't think that's the problem, Rarity."
"Trust me," the Doctor said, "I've like to stay, too. But there's something I've been putting off for too long now." He sighed, then whispered, "I'm going to die soon."
The group shared a hushed gasp. "D – die?"
"It's not so bad, really," the Doctor explained. "Time Lords regenerate, you see. I'll change a little – a new face, new body, new quirks. But it's still me, just different."
"But if all that changes," Twilight said, "it won't be you."
The Doctor sighed again. "Yes, that's the thing. It's never easy to let go of that – I would know, I've done it nine times already. And I've gotten awfully fond of this one."
The room fell silent before Rainbow Dash spoke up. "…you'll still remember us, right?"
The Doctor smiled. "Yes."
"Then you'll come back, right?"
The colt nodded. "Yes, I will. I Pinkie Promise, even."
"And you'd better not break it!" Pinkie cried. "Cause if you do, so help me Celestia, I will find you and drag you back here myself!"
The group laughed, pausing again before beginning to say their goodbyes.
"Keep y'self safe, Doc. We still have to settle that bet, ya know." Applejack dipped her hat. "If ya need it, there's always room for you at the Apple family table."
As the Doctor turned away, Pinkie took that opportunity to put her face inches away from his. She held it there for a moment before saying "FOOOREEEVEEERRR," and then happily bounced away.
Fluttershy slowly walked over. "Well…um…I guess…goodbye."
The colt hugged her gently. "Goodbye, Fluttershy."
As he pulled away, he saw the faintest blush on her cheeks before she shuffled away.
The Doctor grinned and turned to the next mare – "Rainbow Dash, are you crying?"
The pegasus quickly sniffed. "W – what? No! Of course not! I'm not sad!" She sniffed again and wiper her eyes. "I'm just, just – just go already!"
Eyebrows raised, the Doctor nodded and walked to Rarity.
"Doctor," she said simply.
"Rarity," he replied.
She shifted her weight, as if unsure about something. Then she said, "Oh, fine," pulled the Doctor's head and kissed him.
The other mares' jaws dropped as they gasped. After a few seconds, she released the colt and said, "There. Now I have no regrets." And she walked off as if that was that.
The Doctor coughed as he futilely tried to fight the intense warmth on his face. "Well, if that's it, I'll just be off, then – "
Between him and the TARDIS stood Twilight Sparkle.
"Ah, Twilight, of course! How silly of me to forget. Especially since you were the first pony I met, and – "
He staggered slightly when the purple unicorn wrapped her arms around his neck. "Please come back," she whispered.
He smiled and hugged her back. "Don't worry, Twilight Sparkle. I will."
She released him and went to stand with the others. The Doctor looked upon the six ponies he had gotten to know so well, all with tears in their eyes (some more than others; Rainbow was still fighting hers, and Rarity looked as if she was going to break down any second.). Wordlessly – as there was nothing to say that hadn't already been said – he nodded to them and walked into the TARDIS.
As soon as the box was in the Vortex, he let out another sigh. He had discovered a whole new world, with many new species and even its own science. He had seen a nation survive war and treachery to become an utopia of love and harmony.
And he had made six fantastic new friends he would never, ever forget.
The Doctor smiled. Yes, he would definitely visit them again.
…OR IS IT?
In the city of Canterlot, there is a garden, just outside the castle proper. It is a marvel of nature, filled with flowers and animals from all over the country and the planet. It is also home to a collection of statues of various beasts, even some which have been extinct for centuries.
Of these statues, one in particular stands out. It depicts the strange creature known as the draconequus, of which there is only known to only have been one in all the history of Equestria. This statue shows him in all his chaotic glory, but in a position that shows great shock, almost as if he had been frozen alive.
Unknown to the ponies of the city, underneath their very hooves runs a time rift, from which temporal energy leaks into the world. Most of the time, this energy simply passes through and dissipates in the atmosphere, neither harming nor benefitting anypony. But for some time, the energy has taken a liking to that particular draconequus statue, saturating it but seeming to have no effect.
And then one day, that statue gave a tiny crack.