This story takes place between "The Planet of the Dead" and "The Waters of Mars."
There were moments in the Doctor's life where he would look around his Tardis and feel an uneasy emptiness. The departure of his granddaughter, Susan, the day Sarah Jane left, when Joe Grant went off with another man, the death of Peri, the departure of Tegan, and of course, Rose Tylers fate. All of these farewells had left the Doctor with the same empty feeling. However, ever since losing Donna, the place that he called home just didn't just seem empty, it seemed dead. He had a brief moment of happiness when he reunited a man with his son on Christmas day and stopped a cyberman invasion, but when he met a woman who he thought could refill the hole that Donna had left, it turned out she was nothing more than a thief, and could not be trusted. That had stung him. He was now back to moping about the TARDIS, just running around the universe, unsure if he would alone from now on. He knew that any person he took with him would end up dead, hurt, or changed forever.
Donna had come back into his life when he needed her most. When he just needed a mate, and not a companion who would develop feelings for him. He didn't want to give them back like with Rose, or Jo or even Martha to a degree. No, he just wanted a friend like Mickey or Sarah Jane or Brigadier. That was what Donna was to him, a friend he could see himself travelling with to the end of her days.
Fate was not so kind though.
When you lose a lover, it was supposed to be harder then when you lose a friend. The way the Doctor lost Donna struck at him in a bad way, because she would never remember the great, amazing things she did with him, and she would just return to her old life. The Doctor-Donna was no more. There was a mercy in that, he thought, but it seemed worse in his perspective.
He returned himself to looking over the last thing he had in this entire universe, the last piece of his home, the TARDIS. There seemed to be something wrong with his Tardis this time though, as the screens were showing some sort of weird energy around the machine that was affecting it's trajectory through the time stream.
"Well, that's odd," the Doctor said aloud. He looked over the energy source which was being described by the monitors as unknown. "How is it unknown? That's not possible! You have information on all the energy types throughout the galaxy!"
The Doctor quickly ran around the centre of the TARDIS. He studied the consoles and screens, making sure his ship wasn't in immediate peril. Frustration was building as his brow furrowed. He wasn't able to identify what appeared to be dragging his TARDIS to a new destination. He instead decided to take a new approach and see exactly where it was dragging him to. It wasn't pretty, "How... how is that possible? We closed them all up!"
Before the Time Lords went extinct, they had closed up all the cracks in the universe, however one had slipped past them as about two years ago the Doctor, Rose and Mickey fell through one into an alternate universe and discovered a new race of Cybermen. The Doctor was certain this time he had taken care of it, but according to the scanner, someone or something was pulling him right down into a new crack which had just formed. The Doctor watched the event in awe. "This… this isn't possible! How can someone just rip open the boundaries of the universe like this?!"
It wasn't something he could comprehend or even fight against. He was being pulled down through the crack with no way out. The central console of the TARDIS was starting to set alight and wild sparks began to fly The TARDIS itself was shaking uncontrollably, sending the Doctor all over the place until he landed on the couch nearby. He held on as tight as he could and in watched in horror as his home was thrown around like a ragdoll. he felt helpless to do anything, and all he could do was hope that when the TARDIS landed, that it wasn't damaged to the point where he could never leave from whatever world he was about to land. Then suddenly, it all went black.
The Doctor awoke in an uncomfortable position. He leg was bent uncomfortably and his head was resting on his right arm. He got up as quickly as he could and checked himself over to see if anything was broken. Once satisfied he was relatively okay, he stretched his muscles out trying in vain to ease the pain. With that sorted, he quickly looked over his precious TARDIS for the same reason. "Nothing broken... well, at least nothing I can't fix. Everything in working order, good." He mused happily.
He looked over everything a second time to be sure ,and again the TARDIS was telling him it was functional, so his attention was then drawn to the TARDIS door. It wasn't like last time when they were stranded and they had to venture outside to have a look at the situation. No, this time he could just leave right now and no one would be the wiser. Still, he couldn't look away. There was something drawing him to the door.
He could be in some lost dimension, a place that never was or never would be. Despite this, he couldn't help himself when there was an opportunity for adventure to be had, and for the first time in a while, he smiled to himself. It was a smile he always gave when he felt something good was about to happen, so he grabbed his brown jacket, wiped his face with his hands, and he opened the door to the TARDIS on his way to a new adventure.
As soon as he opened the door he could tell that he was in some kind of tree. Iit had been hollowed out to make what appeared to be a library. The Doctor let out a whistle. "Wow. Now this is interesting."
The Doctor looked down to see what looked like a purple pony in front of him. The pony had her mouth open, staring wide-eyed at the Time Lord. The Doctor was immediately fascinated by this creature, and in his usual manner, he put on the biggest grin he could and said "Hello!"
She looked familiar to the Doctor, however he couldn't place his finger on where he had actually seen her before. He got down on one knee, facing a visibly shocked pony. He brought out his sonic screwdriver to check her biology in order to ascertain that what he was seeing was indeed real. The pony in front of him backed away a couple of paces in fear and as soon as the Doctor finished, he felt the need to apologise "Sorry about that. Just needed to see if you were real. i tend to met a lot of colourful holograms that want to kill me. No offence."
He examined the analysis further, and some unexplained energy began centring on the horn of what the Doctor guessed was a unicorn. Suddenly it hit the Doctor exactly what he was dealing with. He had spent a long time learning about popular trends on earth, from music and the Beatles, to books and the Harry Potter series. But one thing that he also remembered was popular cartoons. Transformers, Family Guy, Ducktales, and of course My Little pony: Friendship is Magic. Even the Doctor was a fan of this colorful show, and he was truly loving this. This managed to make his smile grow wider. "Why hello there, Twilight Sparkle."
Upon hearing her name, Twilight finally managed to shake off her shock enough to get a sentence out. "Okay. I want you to answer four questions for me. One, who are you? Two, what is that blue box? Three, what are you doing in my library? And four, how did you know my name is Twilight Sparkle?"
The Doctor stood up, now looking down on her. He rested a hand on his TARDIS.
"Oh that. That's just nothing... well nothing important anyway, well nothing dangerous anyway. well a little dangerous but still… anyway, I haven't introduced myself, have I? How rude of me, I'm the Doctor."
"Doctor? Doctor who?"
"Oh, just The Doctor."
Twilight now had a chance to scan what she was looking at. It was a bipedal figure that was wearing a jacket and vest combination with a tie and trousers.
"Actually, I have a better question. What are you?" The lavender unicorn asked.
"Oh I'm nothing important. Just a Time Lord, but that wouldn't mean anything to you."
"Would that mean that you control time?"
"No, I just travel through space and time and… I've clearly said too much."
The Doctor realised that Twilight's expression had changed from shock to entranced.
"Oh my gosh, how does your device work? What does a Time Lord do? How many are there of you?"
The Doctor was being bombarded with questions and slowly kept backing up to the door of the TARDIS, readying his escape.
"Miss Sparkle, I would love to answer your questions, however I feel that I have overstayed my welcome. Goodbye."
He quickly opened the door to the TARDIS, ran through it and locked it behind him. He put his ear to the door and could hear Twilight just outside the door. His thoughts drifted to the fact he was in a childrens TV show, a fantasy world. Knowing that there were an infinite number of parallel universes, of course there would be one where this place and all of the characters are real. The Doctor decided the best course of action would be to just leave this time around. Maybe it was recent events that affected his decision, but in the end he knew he should go before he messed something up in such a peaceful world.
He got to the central console again, setting the necessary switches. "There we are. Now when we go through the crack to leave, it should close up behind us."
He looked up and realised that he was talking to himself. He had been so used to talking to someone about all this. He walked slowly to the lever that would send him off back to his universe. He looked up one more time and said quietly to himself, "Goodbye Ponyville."
He pulled the lever down and… nothing happened. The TARDIS didn't move. No noise, no lights, no anything. He looked around and sighed heavily. "Well that's… that's not good. Not good at all."