I'm also using a phone so it may be different than other fimfictions.An Unexpected Landing (AKA Pilot)
The TARDIS was in flight, well it was a crashing flight pattern after being shot by the Dalek mothership leaving the Doctor helpless as the cloister bells tolled.
“Damn.. all of the flight controls are out" the Doctor said in a panicked and angry tone as the all too familiar golden energy emitted from his hands.
“Now of all times to regenerate” he sighed “It HAD to be now" his now clearly angry voice bounced off the walls of the straining TARDIS as the Dalek mothership shot the TARDIS damaging it more.
The Doctor, who was now very weak, pressed a button for the Ion Laser Cannon that was mounted to the top of the police box to badly damage the mothership as his last move this face would ever make.
“Well then Allons...y" he strained to say as he was beginning to regenerate completely and streams of gold colored energy began to erupt from his hands and head.
As the Doctor regenerated he started to think ‘what face am I going to get now?’ right when the streams got to their heaviest the Doctor started to yell out in pain as his face started to change as the TARDIS broke through the atmosphere and was now headed toward Ponyville.
Meanwhile in Ponyville
“Move that cloud to the left" Rainbow Dash said gesturing with her hoof as one of Ponyville’s oddest pegasus moved it “So did you figure out how to get your Cutie Mark yet?” Rainbow asked her shy and distant friend Clara.
Clara could only shake her head as an answer she could never figure out how to get her Cutie Mark she was always a black flank for as long as she could remember.
“You could at least speak to me” Rainbow huffed “You're quieter than a mouse most days" the cyan mare truthfully said being that Clara could out shy Fluttershy any day of the day or year.
Clara only lowered her head as a response to her outgoing friend “Hey I didn't mean it that way, you just need to open up more” Rainbow, after saying that remembered that she pinkie promised to help Pinkie Pie with her decorations for a party.
“Shoot I've got to go help Pinkie with her party, just keep working with the clouds then you'll have the rest of the day off.” Rainbow said in a very hurried tone.
After Dash left there was a very strange metallic noise she just couldn't describe at all, but she could tell it was moving very fast toward her in fact.
Her eyes went wide as a blue box busted through the cloud she and Rainbow were working on and grazed her mane.
As the TARDIS came to a complete stop it not only attracted Clara, who was now flying down to the TARDIS doors, almost the entire town of Ponyville came to see the blue box that landed almost perfectly in the outskirts of town save for a bench being knocked over.
“ANYTHING COULD COME OUT OF IT, EVERYPONY RUN!” A very over dramatic Lily screamed, and sure enough that caused all of the ponies in the area run.
Clara wanted to run, but her curiosity was getting the best of her so she knocked on the door hoping nothing bad was going to come out of the box.
The doors swung inwards revealing a light brown stallion with a blue and light blue transitioning mane and a yellowish gold tail that started of light at the base and darkened further down.
Looking closer showed that he had an odd eye color, or colors in this case as he had rainbow colored eyes.
He also wore a black suit that looked a little uncomfortable being worn on the strange pony the sight of the pony also calmed down the ponies who started to run minutes earlier.
Clara also noticed he was staring at her and getting closer to her as with every step Clara stepped backwards until she bumped into the side of a house.
At this point the brown and creepy stallion was inches away from the shy pegasus as she started to fear what was to be done with her.
“Oh hello, where are my manners?” The odd pony said “Hello I'm the Doctor and who are you?”
“Doctor Who?” Clara asked
“That's a dangerous question, let's just keep it at the Doctor.” The Doctor said observing the black pegasus, now what the Doctor couldn't figure out what was wrong with her so he went through a mental checklist out loud.
“Equine, pegasus, blue and red mane and same with the tail, purple iris and pupils, black with… blue stripes? What?” The Doctor questioned “Do equines’ have stripes now?” The Doctor was still in questioning as his eyes were darting up and down to get a good look at what he assumed was female when Clara spoke up.
“U-um s-sir could you please back up ummm just a little bit" Clara tried to say without stuttering, but being as shy as she was she failed.
“Oh… sorry" The Doctor backed up a bit “What's your name again?” trying to remember what she said her name was.
“Clara" she said “Clara Nightwing” She squeaked her full name the second time.
After hearing the name the Doctor felt like knives pierced his hearts “C-Clara? I knew a Clara” He said as he visibly froze in place.
Clara was very confused with his pronunciation “No It's Clair-a not Cl-Are-a” she corrected him.
“Sorry… Clara” he corrected himself after what he was told “They just sound alike to me"
Clara was a very forgiving pony and since she just meet the ‘Doctor’ she could forgive him “It's fine, we all make mistakes.” She assured him.
“Even if we don't like them" the Doctor whispered to himself “Now then I haven't got to do a proper body check yet" he said aloud not paying any attention to the Dalek mothership that just entered the atmosphere.
“EVERYPONY RUN!” A frantic Rose Luck who saw the mothership yelled at the top of her lungs, that however did not get the Doctor’s attention.
“Eyes, nose, hair… still not ginger, I have a tail in this face…, legs… I have four legs… not the worst face I've had at all.” He said done with his body check “Okay done now where was I?”
“Ummm Doctor what about that in the sky?” As she points upwards to the falling ship.
“Ummm… not a clue for the moment at least.” The Doctor said almost in deep thought “I have a plan… I'll need a new sonic screwdriver after this but it's better than having your planet completely destroyed.” As pulled his sonic screwdriver out and started to mess with the settings.
“Doctor what are you doing?” Clara asked very frantically “We're about to be killed!”
Then the Dalek motherships communication speaker activated and addressed the Doctor directly “DOCTOR” the booming voice said “YOU SHALL BE EXTERMINATED!”
“What!” Clara screamed
“I've got the settings right with seconds to spare.” the Doctor was enthusiastic, about this as almost nothing goes his way. “Well then Allons-y!” He said activating the sonic screwdriver that out a force field around the mothership and started to push it back, and a few seconds later the ship was back in space, crippled but in space no less, the sonic screwdriver did not survive and was destroyed beyond repair.
“What the hell just happened?” Clara asked no one in particular “I've seen weird things but not as weird as that.” She told herself but the Doctor acknowledged her.
“That was a normal day, for me at least but don't worry I'm a professional.” the Doctor reassured her.
“Okay but I want only a few questions answered" Clara’s voice was just loud enough for the ponies who were gathering around the phone box again heard her.
“It's nice to see you're talking to a stallion now Clara.” Rainbow Dash said after just getting back after seeing the retreating ship though her comment made Clara blush a brick red.
“I-I-It's not like that" Clara squeaked “Me and him just met” As she pointed to the Doctor, who wasn't paying attention at all.
‘I could have sworn that she was Clara from my earlier travels’ the Doctor started to think ‘Guess not’ he thought as he was ripped from his thoughts by a cyan pegasus.
“Hello? Anypony home?” Rainbow asked “He's an odd one” She told Clara.
“Oh hello, I was lost in thought I'm the Doctor how are you?” He asked Rainbow
“Only as awesome as ever" Dash replied
“Good, but I have one question for you.” He said in a troubled tone.
“Shoot.” Dash said curious about what he would ask.
“Why are you all going dark?” The Doctor asked as he started to feel lightheaded.
“Somepony help him he's going to faint.” A random pony said as the Doctor started to black out, luckily Clara caught him on her back in time before he hit the ground.
“Clara take him back to your house.” Rainbow demanded “Just don't do anything funny to him.” Dash told Clara before leaving a very flustered mare behind with a few giggles in the crowd.
Clara’s house was more of a cottage that resembled Fluttershy’s cottage however it was just deeper in the Everfree forest and closer to her friend Zecora’s as she was more of the shut in type of pony so she couldn't hurt anypony.
Clara shuddered at the thought after that…. one incident a while back…. she was against killing, but that one stallion forced her hoof to kill him in turn caused her to move to the Everfree Forest out was worse than the demon incident with her a very long time ago.
The black mare approached her cottage with the Doctor still in tow she opened the door and made her way upstairs to her bedroom to put the knocked out pony… the Doctor was a very strange pony if she had to say so herself.
As Clara laid the unconscious Doctor on her bed she couldn't help but worry about him so after a few minutes she decided to get a salad and cup of tea and watch over him for the night hoping that he would be alright in the morning for her to get answers from him.
A few hours passed and Clara had finished eating about an hour and Celestia’s sun was setting and Clara was getting tired already and she sighed as her head rested on the side of the bed as she quickly dosed off.
About midnight
The Doctor woke up with a start and saw that he was in a bed…. ‘Whose bed is this’ he thought as he looked to his right to see a sleeping mare.
Being the man... or stallion he should say he picked the sleeping mare up carefully and placed her right next to him on her right did setting as she was facing that way already before covering her up and falling back asleep again.
Clara woke up shortly after wondering what happened to her looking in front of her she saw the cup of tea and reached out for the cup, it was cold to her hoof but it didn't lose it's smell so she placed her hoof back under the blankets……. ‘Blankets?’ She right as she now noticed a warm object behind her she turned to see the Doctor behind her fast asleep and a light blush came to her in the darkness ‘what did I do’ she thought trying to remember what she might have done.
Not wanting to think about it any longer she turned back and tried to fall back asleep not wanting to think about those things just yet and she whimpered lightly as the Doctor turned over and placed a hoof over her as this caused her to fall asleep as his warmth got to her.
Clara dreamed of finally having a stallion to love that wouldn't try to take advantage of the shy and forgiving sides she had and the Doctor finally got in her head and appeared in her dreams, not that she minded it though, it was nice to see him so… so handsome.
Clara realised that she was getting way too close to him in such a short amount of time even for herself as shy as she was, but there was something more to this pony than what his words said about himself she completely fell asleep on the fact that she would have her answers tomorrow and the Doctor's embrace also helped her calm her thoughts.