Doctor Whooves and Fluttershy

by Doctordude2010


The Blue Box Part 2

The Blue Box Part 2

Fluttershy and Rarity stared dumbfounded at the new room they were now in. Where the room was once lit up a bright orange and the console was off center, was now a spherical gray room with the console in the center. It was not as appealing to Fluttershy as the other had been, but she still liked it.

After the mares got over their initial shock, Rarity spoke up.

“Umm… just who is sexy?” she asked the Doctor with a raised eyebrow.

The Doctor blushed and told her quickly, “The TARDIS. Her soul was deleted and stuffed into a human body to die off. Luckily I was able to get her back inside and she killed off the entity that had tried to kill her.

“She insisted that her name would be Sexy, so I've called her that ever since.”

They all heard the TARDIS let out what sounded like a low groan.

“Right, so now that I've got some new threads let's get back to the others.” the Doctor said as he started the takeoff procedure.

Finally he got to the last two levers and asked Fluttershy to help him. He showed her which lever to grab as he grabbed the second.

“Ready?” he asked the shy mare.

Fluttershy looked up at him. “R-Ready.” she replied.

“Geronimo!” the Doctor yelled, as they flipped their controls in unison.

The Vworrping noise was heard again and the TARDIS took off. Fluttershy looked up at the ceiling and noticed the top of the console was spinning in three opposite directions. Not only that, but the lights circling the room were spinning as well.

She looked over and noticed Rarity’s face held the same expression hers did. With a small giggle, Fluttershy walked over to a seat near a separate console and sat down. The Doctor was busy tinkering with the new controls to his ship.

Soon the Vworrping sound was heard again and the TARDIS landed with a thud that slightly shook the room. The Doctor walked over to the doors, opened the left door, and looked out.

“Whoops. Just missed it.” she heard the stallion say. “From the research I've done on this world so far, I think we're in Canterlot.”

The Doctor had barely backed away from the door when a white and purple blur bolted out the door.

“Canterlot! Oh sweet Celestia, we're in Canterlot!” Rarity announced excitedly.

“What did you bring us here for, ey?” the Doctor asked as he looked at the console.

Before he could say anything else, the TARDIS door shut on its own and they took off again, leaving the fashionista behind. Once the room stopped shaking, the Doctor looked at the TARDIS with an annoyed expression.

“Why did you leave her there!?” he said angered by his ship's rudeness.

One of the monitors on the console showed him his answer. Rarity was running at full gallop down the sidewalk.

“Oh sweet Celestia, I forgot about my big fashion show tonight. Thank you Doctor!” she yelled as though he could hear her, and he could.

The TARDIS let out another groan which (to Fluttershy at least) sounded almost equally annoyed. The Doctor looked away from the monitor and ran a hoof affectionately down the panel next to him.

“You could have told me you were gonna do that.” he said jokingly.
________________________________________________________________________________________________________________________________
“OK…. So you guys went back in time to the day Rainbow Dash did her first Sonic Rainboom?” Spike questioned.

The four mares in front of him nodded in approval.

“Why? I mean me, you (he pointed at Twilight), and Starlight saw that Rainboom enough times to fill a book on the details.” he said.

“Rainbow Dash wanted proof that that blue box was a time machine. So, he only took us there to make a point.” Twilight told her assistant.

Before Spike could ask anything else, he was cut off by the Vworrping sound he heard before. He watched as the box slowly came into view and then became solid. The doors opened and Fluttershy stepped out, followed by the stallion he saw earlier.

“How long were we?” the Doctor asked Twilight.

“About…. 3 minutes.” she replied.

The Doctor then noticed the small purple dragon next to Twilight.

“And who are you?” he asked the dragon.

“I'm Spike. Who are you?” Spike asked.

“I'm the Doctor.” the stallion replied.

It was then that he noticed the sixth mare in the room. Twilight seemed to notice where he was looking.

“Oh my, I'm so sorry. Doctor this is Starlight Glimmer, my pupil.” she said as she motioned for Starlight to come forward.

“Nice to meet you.” Starlight said as she shook hooves with the Doctor.

The Doctor then noticed the table in the center of the room. Curious, he walked over to the table and touched it. He didn't expect to be blinded by a bright light and a shock that sent him into the wall at the far side of the room.

His vision quickly returned to him and he noticed the table had turned into some kind of… map. He slowly walked back to the map and looked at it.

“Was that supposed to happen?” he questioned the purple alicorn.

“I don't think so.” she replied and walked up next to him.

The Doctor pulled out his Sonic Screwdriver and began to scan the map.

“This map is connected to every part of Equestria.” he stated as he read the readings from the screwdriver. “Let me try something.”

He held the screwdriver (which was emitting a higher pitched buzzing noise now) next to the map. Suddenly, a large Rainbow colored beam shot out of the middle of the map and connected to the TARDIS. There was another bright light and then nothing else happened.

The Doctor looked at the TARDIS just to see it fade away into nothing.

“Oh no… I knew I should've turned that off!” the Doctor scolded himself.

“Where'd the TARDIS go?” questioned Fluttershy.

“I don't know.” he told her. “How could I have been so careless, I just got her back!”

“Everything's going to be OK Doctor.”

“We can help y'all find it.” AJ spoke up.

“You don't understand tracking down a TARDIS is next to impossible.” the Doctor told the farm pony.

It was then that they all heard a noise like a radar come from the map.
_____________________________________________________________________________________________________________________
“What are we gonna do now boss?” asked a large green dragon.

“Relax. We just robbed 5 ponies and got 16lbs of jewels from some Diamond Dogs, we can take a break.” answered a slightly larger red dragon.

Garble had always not liked ponies, but had hated them even more when his nemesis Spike had brought pony friends into their midst. He had been wanting to get revenge for a long time, but had no way of finding them.

He closed his eyes and was about to take a nap before another dragon walked into the room.

“Garble, we have a situation.” the other dragon said.

“What are you talking about?” said an annoyed Garble.

“Something has appeared at the entrance.”

“What is it?”

“Its some sort of blue box boss.”

“Bring it in here.” Garble told him.

“OK boss.”

The other dragon took off and after a few minutes came back into the room with a large blue box.

“Open it, I want to know what's inside.” Garble told the dragon, getting slightly intrigued.

The dragon he ordered placed both sets of claws on the doors and pulled… nothing. He then pushed the doors… nothing.

The dragon was starting to get irritated and began pushing and pulling harder and harder. The doors simply wouldn't budge.

“Move over you idiot!” Garble said as he got up and walked over to the doors.

After several minutes of struggling with the doors he fell back in exhaustion.

“What is this box made of?” he questioned to the dragon who brought the box in.

“It's wood. Solid wood, boss.”

“Well whatever this thing is, it has some major power coming from it. This box might be just the thing we can use to get revenge on those ponies. That group of ponies are always searching for objects with magical power. It's perfect bait!” Garble finished with a low growl and a sly grin on his face.

“Those ponies have no idea what their getting into.”
________________________________________________________________________________________________________________

“That's strange, that hasn't happened before.” Twilight said with a puzzled look.
Twilight, her friends, and the Doctor were all looking at the map with confused expressions. The Doctor noticed a flashing blue rectangle at a corner of the map that Pinkie Pie happened to be occupying.

“There!” he exclaimed and pointed to the spot with his hoof. “I think that's the TARDIS, it has to be!”

“Uh-oh.” Twilight said when she recognized the location.

“What?”

“That's Mt. Hooferest, the tallest Mountain in Equestria. Only two ponies are known to have made it to the summit, and that took seven weeks.” she explained.

The Doctor, who had to stifle another laugh at the horse puns, responded with, “Yes… but records are meant to be broken, are they not?”

Rainbow Dash laughed a bit and flew over to him, putting a leg around his shoulder.

“Hehe I knew I liked this stallion for a reason.” she said, as she squeezed him a bit.

The Doctor broke from her grip and walked over to the map. He took out his screwdriver, scanned it again, and the image on the map disappeared. His screwdriver begin beeping and a hologram of the TARDIS floated above the emitter.

“Brilliant, now we can track the TARDIS’s signal from the screwdriver. In hindsight I really should've done this ages ago.” he told no one in particular.

He then turned to Twilight.

“How fast can we get there?” he asked her.

“In just a few minutes.” she replied.

“Excellent. All we need now is some gear.” he told her.

The Doctor then noticed Pinkie ruffling through her mane like she was trying to find something. The Doctor’s jaw dropped yet a third time that day, as Pinkie pulled out multiple sets of helmets, goggles, suits, climbing gear, and a cupcake from her puffy pink mane. He made a mental note to himself to do a scan on Pinkie when he got the TARDIS back.

He blinked a few times and then started getting dressed. After a few minutes of cursing and bruised hoof tips, him and the others were ready to go.

“Ok, every pony stand still.” Twilight commanded as her horn began to glow.

Everyone immediately froze in place as Twilight’s horn began to light up. The Doctor heard a low humming sound, but it was gone a second later. As he opened his eyes, he took in his new surroundings.

He looked around and saw his friends a few feet away from him. He took a head count and realized somebody was missing. He looked around and saw Fluttershy lying right next to him.

He looked down at his new companion and smiled. He felt a tap on his shoulder and turned around.Twilight and the others had gotten up and were now waiting for him to lead the way.

He turned around, picked up Fluttershy, and set her on his back. He then took out his screwdriver and activated it. The standard buzzing noise was heard, followed by a steady beeping sound.

He moved the sonic around until the beeping increased. After he put the screwdriver away him and his new friends set off in the direction the sonic had indicated. The Doctor, still not used to his new pony form and carrying Fluttershy on his back, struggled to keep moving.

After awhile though, his legs buckled, and he fell face first into the snow covered ground. Everyone figured that the might as well stop and take a break. Using her magic, Twilight formed a medium sized cabin from nowhere.

They all walked inside and sat in front of the fire in the fireplace. The Doctor, however, was sitting in a corner by himself. He had wanted to sit down and think about everything that had happened during the past few hours, but hadn't been able to find the time.

As the sun began to set, they all agreed that it would be best to wait till morning. Eventually, everyone except the Doctor and Fluttershy were fast asleep. Fluttershy, who was unconscious most of the day, was not tired and the Doctor didn't sleep very often.

Fluttershy stood up and walked over to the Doctor. She tapped on his shoulder gently and he turned around to meet her gaze. She wanted to ask some questions.

“Umm Doctor. May I ask you some questions?” she asked him shyly.

“About what?” he asked her in reply.

“Well… more about your planet. Where you come from.”

“Very well. Like I said before I’m from a planet called Gallifrey. My species is called Time Lords and also, as I said before, I have two hearts. Timelords have a very extensive life span and each is given 13 lives to live.
“If a Time Lord is going to or about to die, they can regenerate. I don't mean just healing either, our face, body, thinking patterns, organs, everything is changed at complete random, so you never know what you'll get next. You could become wise, grumpy, funny, young, old, anything, but you’d still look like a human, or I guess pony in this situation.”

He paused and looked over at Fluttershy expecting her to not be paying attention like others would do, but she simply stared back at him and nodded her head for him to continue.

“I trained at the Time Lord academy and had a great life with my granddaughter Susan. Until one day when I did the dumbest thing I had ever done… I stole a TARDIS and ran away.
“I had all of time and space at my fingertips.. sort of anyways. The TARDIS I stole didn't function properly and I crash landed on earth with Susan. When I managed to get the TARDIS working correctly, I left her in 1963 so she would be safe and could live a normal life like a human.”

Fluttershy scooted closer to the Doctor and wrapped her legs around him in a caring embrace. The Doctor was startled, but slowly joined the comforting embrace. After a few moments of this they pulled away from the hug and Fluttershy asked him a simple question.

“What happened to Gallifrey?”

The Doctor said nothing for a few moments, then slowly looked away from her as he recalled his memories from the last moments of the war.

“Before I tell you this Fluttershy, you have to realise that I had no other choices/options than this…… Gallifrey is gone because I….I..I..destroyed it.”

He heard a faint gasp come from Fluttershy and felt her draw back slightly.
“When I started calling myself the Doctor I made a promise to myself and to the universe that I swore I would never.. ever break! One war, however, was enough to make me forget that promise. A war that would silence the universe for decades to come… The Time War.”

Fluttershy was on the edge of her seat waiting for the Doctor to continue, but he just looked at the floor with regret in his eyes.

“Well I think I should try and get some sleep for tomorrow,” Fluttershy finally spoke up, “ we've got a long walk ahead of us.”

“Yeah. I'll see you in the morning Fluttershy. Goodnight.”

“Goodnight Doctor.” she finished with a yawn as she closed her eyes and let sleep take her.
________________________________________________________________________________________________________________
Fluttershy didn't know where she was. She was floating around in a large, empty space. Occasionally images would flash past her and she could hear voices.

One image in particular showed a large group of dragons standing around her and trying to open her doors. Wait, doors? Since when did she have doors and when was she shaped like a box?

Before she could ask more questions, a dark blue earth pony appeared in front of her.

“TARDIS to Fluttershy… TARDIS to Fluttershy… come in… can you hear me?”

Fluttershy nodded her head quickly and tried to speak, but couldn't.

“This is an emergency telepathic messaging signal. I can use this to help you, but it only works once. When you wake up tell the Doctor that I am in the hands of some rather obnoxious dragons, so he'll want to have some help with him.
“Also tell your friends that they are in danger as well… these dragons are using me as bait to lure you guys here. Good luck Fluttershy!” the blue mare told her.

She then faded away and everything became fuzzy. Everything disappeared and Fluttershy snapped her eyes open.
_____________________________________________________________________________________________________________________
Fluttershy looked around, she was back in the makeshift cabin Twilight created. She got up, stretched, and looked outside. The Doctor was sitting right outside the door to the cabin, talking to Rainbow Dash.

She didn't want to be rude, but what she had to tell him was important. She stuck her head through the door, asked if she could talk to him, and led the gray stallion to the breakfast table. She told him what she had seen and what the TARDIS had warned her about.

“Oh brilliant! That definitely helps us to be prepared. I'll go tell the others and we’ll come up with a plan.” the Doctor said as he walked off to find the others.

“Dragons? The only group I can think of that would be looking for us would be the dragons we met during the dragon migration in Ponyville.” Twilight explained.

“I haven't been in your world for very long, so could you inform me on dragon behavioural patterns?” the Doctor asked Twilight.

“Of course, just let me get my books on dragons.”

With that, Twilight walked over to her bag and began looking through it. The Doctor noticed Fluttershy staring at him, but she looked away as he looked at her. Almost immediately, the Doctor stood up and walked over to the shy mare.

“Are you alright Fluttershy?” he asked quietly as he sat down beside her.

“No… I'm just still thinking about everything you told me last night. You never told me why you did it.. blew up Gallifrey.” she replied, her face hidden behind her mane.

“I did it because I had no other choice. I used every method I knew possible to avoid doing that, but everything I did to help didn't make any difference. I fought in the war… for hundreds and hundreds of years I fought.
“I watched my people dying…children..dying… I thought it would NEVER end! Until one day, I snapped and did the very last thing that a would ever do! I broke my promise… 2.47 billion children on that planet and they never lived their full lives!”

Tears began swelling up in Fluttershy's eyes as the Doctor continued. Finally, the dams broke, and Fluttershy began sobbing quiet enough only the Doctor could hear her. Or so he thought…

“Fluttershy, are you alright, is everything OK!?” Rainbow Dash asked from outside.

The door was suddenly kicked open and RD flew over to her crying friend. She comforted Fluttershy while telling her that everything was okay, and that she was there for her. The Doctor stood to the side, watching the scene in front of him take place.

After Fluttershy stopped crying for the most part, the Doctor started to move toward her again, only to be blocked by a very fast and very angry Rainbow Dash.

“Now you've done it! Now you've really done it! How dare you make Fluttershy cry like that! Believe me… you're gonna wish you were a unicorn right now, because I'm about to show you what happens when someone makes my best friend cry!!!” she yelled at him.

The Doctor stared right back at her and could swear he saw miniature daggers coming out of her eyes. RD landed in front of him with a hard crunch and pulled her hoof back. The Doctor closed his eyes as he prepared to feel the punch of her hoof against his face.

Nothing happened. The Doctor opened one eye to see Fluttershy holding back RD’s hoof rather successfully. She had a look of concentration on her face as she somehow pulled the cyan hoof to the ground and stood on it.

“RAINBOW DASH!!! LISTEN TO ME!!!” Fluttershy yelled at the cyan mare, who immediately complied. “It's not the Doctor's fault that I started crying. It's my fault, I wanted to know why he destroyed his home, and I forced it out of him!”

The others came in after a few moments.

“What in tarnation is goin on in here?!” AJ asked, looking at the three of them.

“O-Oh! Nothing really.” Fluttershy said, her timid nature returning.

“The Doc was telling Fluttershy about how he destroyed is home planet.” RD said flatly before Fluttershy could stop her.

“Ah don't wanna know. Anyways, Twilight told me tuh come and get yea Doc. She found those books on dragons you wanted.”

“Excellent. Well, tell her I'll be down in a moment. I need to speak to Fluttershy in private for a moment.” the Doctor responded.

“Sure thing.” AJ said as she left the area of the cabin, dragging a reluctant Rainbow Dash by the tail.

“Fluttershy I'm sorry, I didn't mean to go that far. I ju-” the Doctor's apology was cut off as Fluttershy embraced him in a nice, long hug.

“It's OK Doctor. I just wasn't prepared for hearing that much info.” as she finished, she gave him a sweet, warm, and reassuring smile.

The Doctor smiled back at her as he followed her to where Twilight was currently sitting, muzzle deep in a book. He went to sit with her, while Fluttershy went to find Rainbow Dash. When she found her, they shared a very heated conversation.

“OK Fluttershy, just tell me one thing. How much do you trust that stallion in there?” RD asked her.

“I trust him plenty Rainbow Dash. He hasn't done one thing to hurt me at all.” Fluttershy replied angrily.

“You haven't known him very long!”

“I don't need to… I can see it in his eyes. He's seen so much… lost so much.. and I can see the honesty in his eyes. I trust him because he's honest, kind, and loyal! I see more loyalty in him than you could EVER have!” Fluttershy finished, as she walked away from the cyan Pegasus.

Rainbow Dash hovered motionless in midair, not believing what she had just heard her oldest friend say to her. Her anger was quenched into sorrow and a hurt pride as she landed on the floor of the cabin and walked over to her temporary bed. She was mad at Fluttershy sure, but she didn't want to make Fluttershy blow up at her like that.

Fluttershy, meanwhile, was in her spot by the window crying her eyes out. She didn't know what had come over her when she yelled at Rainbow, but she never wanted it to happen again.
___________________________________________________________________________________________________________________________
Outside Cabin, Early Morning

Everypony woke up early the next morning and got dressed and ready to move on. Fluttershy and Rainbow Dash didn't say a word or look at each other most of the day. Each time they would try to apologise to each other, they would relapse back into silence or they would chicken out.

After a while, the Doctor stopped walking, causing the others to ram into him.

“OK, the TARDIS's signal is getting stronger. It shouldn't be more than a few feet away.” the Doctor said while scanning with the screwdriver.

He looked up and saw a large cave inside of the mountain face. They continued walking until they were just in front of the cave entrance. The Doctor peered into the cave and saw the TARDIS sitting a few feet away in the middle of the cave.

He began to cautiously walk towards his ship. Just as he got near it, he heard screams come from behind him. He whipped his head around only to have a large rock smack him in the face… hard. The last thing he saw, was Fluttershy running towards him before he blacked out.
___________________________________________________________________________________________________________________________
Garble's Office, Late Afternoon

“Wake Up… Wake Up… WAKE UP!”

“Whaaaa? Uh.. my head. Was that really necessary?” the Doctor said groggily.

“No, but it doesn't really matter.” a red dragon standing in front of him told him.

“Blimey that hurts. Wait… No, not the time for this now. Who are you?” the Doctor asked regaining his body functions.

“My name is Garble, I'm the boss here.” Garble answered the stallion's question. “But I'd rather like to know who you are.”

“I'm the Doctor. Now let's cut the act, where are my friends?” the Doctor started.

“Those little ponies and that stupid little dragon spike are down in the dungeon. You'll be joining them soon.” Garble began to walk around the room. “But first I want an answer to a question. What that thing..?”

The Doctor looked in the direction of the dragon’s gaze and saw the TARDIS sitting in the corner of the office. If he could just get over to it.

“Well… I'm waiting.” Garble spoke in exaggeration.

“I don't know. I can't really inspect it from here.” he told Garble.

He did not expect the dragon to pick up the chair he now realized he was tied to closer to the TARDIS.

“Is this close enough for you?” Garble said with an attitude.

“Yes, this will do.” the Doctor replied.

If only he could get Garble distracted long enough to open the doors, get inside, and shut the doors again. Not 2 seconds later, he heard a loud bang, followed by a crash, and then footsteps. The door of the office burst open and a dragon guard ran in.

“Boss! We have a problem, you might want to see this.” the guard explained, breathing heavily.

“Fine. Don't try anything, I'll be right back!” Garble told the Doctor.

“Couldn't think of anything if I tried.” the Doctor said in return.

Garble looked at him a second longer, before running through the door. Once the Doctor couldn't hear the dragon's footsteps anymore, he started bouncing in the chair, scooting closer to the TARDIS's doors. He tapped his hoof on the floor twice and the doors flew open.

He was halfway through the door, when he heard the familiar footsteps coming down the hallway. He increased his efforts in getting through the doors and into the safety of his ship. Just as he got all the way inside, the office doors flew open and Garble walked in.

“OK, now where wer-. Hey! Get back here!” Garble yelled when he saw the Doctor inside the TARDIS.

“Hate to cut this short, but I've gotta run.” the Doctor said with an amused grin as he tapped his hoof again and the TARDIS doors closed.

The Doctor began to scoot backwards towards the console, giving up on trying to get out of the chair, and began manipulating the ship’s controls behind his back. It was difficult, but he managed to input coordinates for the dungeon. The only thing now was to pull the Demat lever.

The Doctor's pupils shrank, as he realized that he couldn’t pull the Demat lever. Thinking quickly he came up with an idea. He would spin himself around while standing on his hind legs and pull the Demat lever with his mouth.

Using the console for support, he slowly began to stand up. When he was standing up, he began to slowly turn himself around. After that was done, he tried to reach down with his mouth.

He was an inch away, before his head stopped moving. He was so close, just one more inch and he could take off. He made another realization and stuck out his tongue.

The flesh connected with the handle and wrapped around it. He began to pull back, putting all his strength into his large tongue. Slowly, the lever started to move.

With one final pull, the lever flew backwards and the Doctor fell to the floor. With the destination set, the TARDIS began to take off, disappearing into thin air.
_____________________________________________________________________________________________________________________________________
Dragon Dungeon, Late Morning

Twilight looked around at her friends inside the cell. They were all chained against the walls and were bruised pretty badly. AJ had a broken leg, Twilight was scraped and bruised, Pinkie Pie hadn't sustained any injuries at all, and.RD’s wings were broken along with her snout.

Twilight finally looked in dismay at the quivering canary yellow mass in the corner. Fluttershy had sustained the most fatal injuries of all of them. Her wings were pulled off from the joints, she had several stab wounds, her mane and tail were cut short, and her face was bruised and swollen.

From what Twilight could tell, she was barely clinging to life. She was praying that somehow the Doctor could save them.

“You're going to be OK Fluttershy, just hold on.” Rainbow Dash told her.

Fluttershy looked up at RD and tried to give her a small smile.

“I.. don't think…. I'm gonna.. get through this… Rainbow D-d-dash… *cough* *cough* *cough*.. It's getting... harder.. to breath..” Fluttershy replied in a scratchy, quieter voice.

“Don't talk like tha’t Sugarcube! You'll get through this, we Pinkie promise.” AJ told her,while, for the first time in many, many years, she let lose a few tears from her eyes.

Then simultaneously everyone chanted 'Cross my heart and hope to fly, stick a cupcake in my eye!’

Fluttershy began to cough harder and seemed to struggle lifting her head up. Warm tears filled her eyes as she looked around at her friends.

“I will always….re-remember… you…...guys….I…..love…..you…...allll……..”

Fluttershy's eyes rolled into the back of her head and she let out a final breath. The others just stared at their timid friend lying on the floor motionless. Before long, they all began to sob.

Pinkie’s hair deflated and went straight past her shoulders, while her entire color changed to a magenta color. RD closed her eyes and let the tears flow. Spike, who was in the cell next to them began crying too.

Twilight, whose heart had broken beyond repair, heard a soft noise. She stopped crying for a moment to listen to the sound, it was getting louder. The others heard it to and they began looking around frantically.

The sound died out and was replaced by another sound, an other worldly sound. It was the most beautiful sound that Twilight had ever heard. They all looked in the center of the room, as the TARDIS slowly appeared out of thin air.

With one final 'Vworrrrrrrrp’ sound, the TARDIS became solid. Everypony’s hearts kept as they waited for the doors to open. After a minute or two, the doors opened to reveal the Doctor tied to a chair.

“Hello everyone, did I miss anything? Wait no, actually could you help me out of this chair Twilight?” the Doctor asked the alicorn.

Twilight nodded, and untied the ropes. After he was free, the Doctor began getting the others free. After he got Spike out of the other cell, he walked over to where Fluttershy was lying down.

“Come on Fluttershy, we need to get you to the hospital. Fluttershy, can you stand up? Fluttershy?”

“She's dead Doctor.” RD suddenly spoke up. “She died five minutes ago, because you didn't get hear sooner!”

The Doctor gave RD a very hurt look before looking back at the canary colored mass in front of him. He closed his dues and reminesed everyone he had lost because of him throughout his years of traveling. “No..”

“No?” RD looked at him.

“NO!!!” the Doctor yelled at RD. “She's not dying on my watch! Not another life, not one day or the next, not ever!”

The Doctor grabbed Fluttershy by the hoof and started to pull her.

“Help me get her into the TARDIS! There may be a chance I can save her!”

Twilight used her magic and carried Fluttershy's body into the TARDIS. Soon, everyone was inside the TARDIS and they took off. When they were in sustained flight, the Doctor walked over to Fluttershy's dead body and touched it with a tender hoof.

His hoof started to glow in a bright yellow aura. The yellow aura spread from his hoof to Fluttershy's body, all the stab wounds were shrinking and becoming nonexistent. Fluttershy's mane and tail was growing back to their original length, her blood was retreating back into her body, and finally, her face began to return to normal, the bumps and bruises going away instantly.

“Is she better now!” RD asked anxiously.

“Not yet, I need to restart her heart.” the Doctor responded.

Putting both hooves on the side of Fluttershy's face, he leaned in closer, until his lips met with hers. As he kissed her, her body began to glow, as regeneration energy coursed through her. Her eyes fluttered open and she stared up into two deep emerald eyes.

She let out a sharp pained breath as the Doctor pulled away. She sat up and looked down at her hooves, they were glowing brighter and brighter. She jumped off the table and stood clutching her chest.

Without warning, she stood on her hind legs and began screaming in pain, as energy coursed throughout her body and she became a large fireball. It lasted roughly 20 seconds before she suddenly stopped glowing and dropped back to all four hooves.

She then felt multiple sets of hooves around her body as her friends hugged her in a tight embrace.

“Fluttershy, I'm sorry, I'm so so so sooooooo sorry!” RD spoke up.

“What for Rainbow Dash?”

“For our fight the other day! I'm sorry! I'm just so glad your safe!” RD cried out, tears of joy going down her face.

“Doctor what did you do anyway?” Twilight asked the stallion.

“Time Lords have this trick, it's a sort of way to cheat death I suppose, I have regeneration energy inside my body. I transfered some of that energy to Fluttershy, and it repaired her body. At the same time, however, when I restarted her heart, I accidentally gave her a little to much energy, and her body tried to fulfill a Time Lord regeneration.
“Before that could happen though, I managed to pull some of the energy back into my body. Everything was repaired though, even her missing wings.”
the Doctor explained.

“Well, thank you Doctor. Thank you so much for bringing her back.” Twilight said.

“Of course, what are friends for.” he replied with a shake of the hoof. “Now let's get you all home.”
________________________________________________________________________________________________________________________________
Twilight's Castle

“Well, here you are princess. Sorry I've gotta leave so quickly, but I think the regeneration energy had a strange effect on Fluttershy. Mind you it's temporary, but I don't know.
“When a Time Lord regenerates, afterwards we become kind of loopy, crazy, or forget who we are for a short period of time. Fluttershy, however, is acting like she's in heat.” the Doctor told Twilight.

“I'd get her home pretty fast if I were you. Last time she was in heat, she chased Big Mac around Ponyville for three days straight.” Twilight explained to him.

“I get the picture.”

“Oh and Doctor?”

“Yes?”

“Fluttershy told me she was gonna start traveling with you. Just please be careful and look after her.” Twilight pleaded to him.

“I promise you, I will never let anything happen to her agai-AHHH! Fluttershy what are you doing!” the Doctor jumped as Fluttershy grabbed him by the waist and started trying to pull him back into the TARDIS.

“Oh don't worry about me Doctor, the only pony who should be concerned is you letting me have my way with you…” Fluttershy told him in a sly and sultry voice, while she looked at him with half lidded eyes.

“Good luck Doctor!” Twilight yelled, as Fluttershy finally pulled him from the door and he disappeared into the ship.

After a moment, the doors slammed shut and the TARDIS began to dematerialize. She watched as it disappeared into thin air.

“He's gonna need it.” Twilight smiled coyly as she went to find Spike to sent a letter to Princess Celestia requesting that they meet as soon as possible.

She couldn't wait to tell her about Fluttershy's new stallion friend.