The Doctor and Rainbow Dash handed their menus back to the waitress at the resteraunt and almost immediately Dash began chatting. "So, 'ya new around here? I've never seen you before." The Doctor looked down at the table, trying to figure out what to say. "Well... Ahem... I was here before. A long, long, long time ago. But, let's not worry about that."
Rainbow just nodded slightly and said "Okayyy. Well then, may I ask why you want me.? It's obvious you don't wanna talk much but..." The Doctor just looked her in the eye and said "Look, you're in terrible danger. You specifically. The Dalek are after you. They have found a way into this world, and they know that you are the key. They will stop at NOTHING to get a hold of you. And, it is my duty to ensure that the Dalek never take another life. So, I am here to protect you." Dash just cocked her head quizzically. "The Dalek? What the heck...?" Dash began to trail off when she saw a shadow move behind the Doctor. "What? What is it, girl?" The Doctor shouted. "Tha-tha-That" Rainbow replied, pointing.
The Doctor turned his head and saw a bug creature, a creature that was pony-like in stature but had the wings of a moth and sharp fangs. "What is that?" He asked. Rainbow cleared her throat and said "A Changeling. they transform into somepony you love and feed off of your love for them." The Doctor continued staring in the Changelings face and said "Good. Because everyon- everyPONY, I loved is dead." The Doctor stared at the Changeling for another minute, and that's when it attacked. The Changeling delivered a powerful blow into The Doctor's chin, knocking him backwards. 'Doctor!" Rainbow shouted, Dashing up (Eh, Eh?). She apple-bucked the Changeling in the stomach and that was when everypony cleared the building.
The Changeling pinned Dash on the ground but she came back by pelvic thrusting it off. She rolled over onto her hooves and flew up, about to go in for a grand-slam. But, the Changeling flew up and kicked Rainbow Dash across the room, injuring her wing,
The Doctor got back onto his hooves and retrieved the Sonic Screwdriver that he had attached to the medallion that day. He aimed his Sonic Screwdriver right at the Changeling while Rainbow Dash was brawling it and he pushed the main button which fired a sonic pulse through the air and knocked-out the Changeling. "Alright, we gotta get a move on, it'll re-gain consciousness soon." The Doctor yelled while he ran towards the exit with Rainbow Dash. "If we can get to the TARDIS, we can escape and do our first task." The Doctor continued, running through the streets of Canterlot with Rainbow Dash.
"The archives are just up ahead!" Rainbow yelled. The Doctor was gasping for air as if he was physically exhausted. Rainbow Dash shot up and said "Hang on." She flew in front of him and he bit onto one of her back hooves and they flew back to the archives. Rainbow landed at the entrance and said "Gee, do you have an alien bite or something?" (Amy pond reference) . The Doctor ran in followed by Rainbow Dash. The Doctor opened the door to the TARDIS and said "Ladies first."
Rainbow Dash walked in and her jaw dropped. "Sweet Celestia. It's bigger on the inside." The Doctor just chuckled and said "I love it when they say that." He approached the console and said "Alright, just to get you acquainted with time travel, tell me whatever destination you would like to go to." Rainbow Dash just stood there, silent, thinking. "Alright... I know where I want to go..."
P.S. Guys, I will become a better writer, trust me. And also, this WILL get more exciting.
Give me a moment, I need to gather my bearings. Word of advice, don't break up the story with author notes. (It's not a very smart idea.) Doing so breaks the flow of the story, and that's something that needs to be preserved. You know who else used author notes? XXXbloodyrists666XXX, and look where that got her. (She wrote my immortal.)
Anyway, now that I think I've gotten in the flow, let's begin. First thing I notice is a lack of description. Now that's all right, you're new, you can't be expected to pump out a full length novel, however, when you barely have enough background to set the scene, that's a good sign that you may need to revise some things. Add a little more flare into things. What does the restaurant look like, what do the characters think of it, what does it smell like? A whole herd of opportunities to add some spice into your writing that you seem to have flown right over.
Next point is spelling. I honestly don't see how this can be a problem in this day and age, but somehow people still manage. Investing in a simple spell checker is going to do wonders for you, as well as sort out a couple of the less then straight sentences. Really, these kind of things should have got caught in proof-reading, which is also a thing you should start doing now that you write here. Always proof read.
Next, every time a pony speaks, they need to get their own line. I don't mean conversational line, like a script, I mean written line. Press enter each time a pony starts to talk. It'll help break up the larger paragraphs and help destroy that chunky flow your story has.
All right, next would be...would be...wow. I don't have a next one. Give me a moment to check back through this.
Nope, nothing next. This is a surprise for me. Good job. I usually find more things wrong.
Moving on, you seem to have a basic grasp of characterization, though a few certain moments do stand out to me as being out of character. Try to imagine whether the character would actually say what you wrote. I personally find that it helps, though it is all speculation. I am a little concerned that you don't know enough about the source materials to tell a fitting story, though I suppose time will tell what happens next.
'Pelvic thrusted it off.'
Nazkan
P.S. The Doctor totally has people he loves, what about Rose? Though I suppose the people he loves would have to be ponies for the changeling to work, so you get a free pass there. Also, Daleks. The Doctors enemies are the DalekSsss.
One question just one question. What happened to Twilight and PC? I don't see the Princess letting somepony as dangerous as the Doctor out of her sight.
699442 Trust me. The Princess has something up her sleeve...
Nazkan's comment covers everything I wanted to say grammar and spelling wise.
I would just like to add, that while I have seen Doctor Whooves traveling with Derpy, the mane six, and Twilight solo, I have never seen one where it's just Rainbow Dash. So, congrats on that.