Dr. Whooves: The Oncoming Storm.

Chapters

Chapter 1: A Whole New World.
Chapter 2: Ponyville
Chapter 3: A Madman Without His Blue Box
Chapter 4: Meet Chrysalis
Chapter 5: Questions Without Answers.
Chapter 6: Goodbyes And What Not.

Chapter 1: A Whole New World.

The same box, same sonic screwdriver, same doctor but it wasn't the same. He was all alone now. Just a madman and his box, off to see the universe. He occasionally visited some old faces and old friends. Though they didn't know him yet, some old, some new, but he knew them all, and yearned for the times he had with them. He missed them with all two hearts that he had. But they were all gone now. It always ended like that, you can't run forever. And The Doctor new that better than anyone. He knew loss better than anyone. He watched as the city of Arcadia fall. His world fall. He watched his people die. All of them, he was the last of the Time Lords. The ancient race of humanoids who kept watch over time and space. He did it as well, he killed them all. Every man, woman, and child on Gallifrey. Perhaps that was the most chilling thing about it all. Him knowing that billions of children died by his hand. A man forced to kill his entire race. And he was cursed to live on. The curse of the The Doctor. He has seen things that would make would-be gods tremble. He has come face to face with the devil himself, and laughed at him.

He lost everyone now, as he always did. Two hearts, and he truly did feel twice the heartbreak. But he lived on, making sure the sacrifices, they made would not be in vain. He witnessed as his wife died as he helplessly looked on. His own daughter died in his very hands. And he stood in horror as his best friend sacrificed herself to be with the man she loved. It had to be this way. It was his punishment for the horror he caused. That in some worlds the word Doctor, translated into great warrior. That he could make armies tremble at his very name. Doctor Who. He saved the universe countless times, and countless planets to match. But he was truly one, if not the most infamous being in the entire universe.

But regardless of the pain he felt. He would never stop, he would save the universe, if he liked it or not. Though he usually did. He was traveling now, no planets that needed saving, no pocket universe that cried for his name. He took the moment of peace for what it was, rest. Though sometimes it isn't just his universe that needs saving. The Doctor was flying his bigger on the inside blue box through time and space. When it made a funny noise.

"Oi well, that didn't sound good. You alright old girl?", The Doctor said well patting his TARDIS control panel. It made the sound again and again.

"The shielding is down?! What?!", he said astonished, what was happening?!

He scurried down beneath his control panels and was investigating the wiring when a sudden jerk flew him across the floor. As he was holding his head, a fire started off in a corner. Suddenly his eyes widened. Only one thing in the universe could bring down the TARDIS shields in an instant without warning, and only one thing could completely fry all his Time systems. The Doctor realized what was happening. He checked the date and place. Before saying out load the startling realization.

"The incident at Karin J-9B... Black Hole vs Supernova...", The Doctor said with a touch of fear in his voice. He knew all too well that no one knows what happened to the star and black hole. Only that what ever happened, it caused a split second fracture in Time.

The TARDIS made even worse sounds as it moaned and groaned as it the fires started to spread. Sirens were wailing, as the TARDIS was being sucked into the Black Hole. The Time Lord was running around the control panel trying desperately to get out of the situation that would surely result in the final extinction of the Time Lords. But it was to avail. The TARDIS outer hull was starting to breach, The Doctor and his blue box were now at the complete mercy of the Time Void itself. The TARDIS wailed as the last security systems completely shut down. The Doctor uttered one last word before it all went to black.

"Geronimo!"

The Doctor woke up on a field. Groaning in pain, and trembling with the horrific agony he was in. He looked at his body, there was a scary amount of blood. He looked at his surroundings, he was in a field surrounded by flowers and trees. This was it, he had to be to far gone for regeneration to kick in, right?. He closed his eyes for a split second. Before hearing a strange voice. It was scratchy, rather rigid, feminine as well.

"Sweet merciful Luna! Are you okay dud-" The voice stopped suddenly, whatever it was, it must have seen the blood and realized what The Doctor already knew. The Doctor uttered one word, his voice cracking with the severe pain he was in.

"Peachy."

His voice trailed on with the word. As his voice slowly gave. The voice seemed unconvinced.

"Woah! Hold on dude, I'll get you out of here and to...!", the feminine voice said trailing.

The Doctor, rolling his eyes painfully at the stupidity that this creature couldn't realize he was dying one way or another. Decided to humor himself given it was pointless anyway.

"I would imagine a hospital would be a fitting place?", The Doctor groaned mentally wishing for a pair of sunglasses, given even with his eyes crunched tight it was still like he was staring at the sun.

"Ya! Duh! Just you know, what are you?!", the voice said.

Great more stupid questions being asked to a dying man. No he shouldn't think that, they're are no such thing as stupid questions. Groaning both in pain and also in frustration. The Doctor said,

"I am a Time Lord, a race of beings you probably never heard of, now please, hospital, or can you leave me to die in peace?!"

"Sorry! Ya here I'll fly you over right now, don't worry we'll be there in ten seconds flat!", the voice said, as it faded into nothing.

The Doctor managed one last word before passing out from blood loss,

"Perfect"

"We did all we can for him, this creature whatever it is. Has a very different anatomy than ponies, Rainbow. I am not sure if we made a difference at all. I'm sorry." Nurse Redheart said.

Rainbow Dash shook her head slowly, "No he'll make it...." Rainbow Dash said slowly, before continuing, "Celestia, I don't even know his name..."

Rainbow Dash looked at the mysterious creature. She didn't even know his name. And here she was watching him die. She refused to leave the room. She slept there and ate there. Her friends came in to see her and the creature. They all seemed to have no idea what a Time Lord was. Twilight Sparkle, an Alicorn princess took the most interest in the strange being. She said it had a similar appearance to that of a Human. But it couldn't be a human, since it had two hearts. The next day Rainbow Dash woke up after falling asleep for a few hours to find the man still in a coma. When suddenly he woke up.

"Wher-, where am I?", The Doctor uttered.

"You're alive! The Doctors said you wouldn't wake up!", Rainbow Dash said with shock.

"Disappointed?" The Doctor said with a laugh. Before groaning with pain.

"Listen to m-", The Doctor continued, before being cut off by the strange creature that was in front of him.

"You must be as tough as I am! Nopony I know could have survived injuries like that! Nurse Redheart said you had some thing called internal hem-hemorr-hag-ging. And the Doctors couldn't do anything!"

"I am not going to survive.", The Doctor said groaning, in frustration at being constantly cut off.

"What! But you woke up! You aren't dying!", Rainbow Dash screeched,.

"I will continue to live, but not in this body, listen to me. This is very" The Doctor said, before crying out in pain.

"You'll be okay! I will get Nurse Redheart hold on!", Rainbow Dash yelled then before she could move The Doctor grabbed her.

"LISTEN! I will regenerate into a new body, it will still be me, but a whole new body!", The Doctor explained, all the while twitching with pain.

But before Rainbow Dash could respond, she saw the impossible. The strange man, body was surrounded in aura of light that seemed to be radiating off his body. She looked away as his body seemed to turn to fire, all the while The Doctor screamed in agony as his entire body morphed into something completely new! When the rainbow maned pony looked back at the man. She couldn't believe her eyes. The strange creature turned into a PONY!

"What?! How is that! How did you! Who are you!", Rainbow Dash yelled at the new brown maned and coated pony that now stood in front of her.

The Doctor jumped out of the hospital bed. And smiled, as he chuckled at his new body.

"Pony? Oi, well that's new. Never been a pony before, come to think of it, I don't think any Time Lord has been a pony. All a bit strange really." The Doctor stated, while moving his jaw, and trotting in a circle. And wagging his tail, and flexing his ears.

"Wait tell me one thing", The Doctor said, he was about to say something when he shook his head and said something else.

"Wait hold on then, I didn't even catch my hero's name. Who are you?

Rainbow Dash stuttered her words, "Uh, my name is. Umm..."

"Umm? That's a strange name, granted I've heard stranger. But Umm, just sounds so boring, tell me Umm, what planet are we on?

Rainbow Dash continued to stare at the mysterious stallion that now stood before her.

"What? Cat got your tongue? Huh, do you have cats here? Oooh, that would be brilliant. Ponies and cats living side by side. Can you imagine?" The Doctor said, laughing.

"We, ya. We have cats, my friend Rarity has one. But no, they are just pets, silly", Rainbow Dash said while laughing. Before getting serious again.

"My name is Rainbow Dash, not Umm, by the way. Fastest Pegasus in all of Equestria, the bravest, the coolest, most awesomest pony", Rainbow Dash said while striking a pose.

"Fantastic I'm sure you are.", The Doctor said while having a huge grin on his face.

"Ya hehe." Rainbow Dash said as she tried to suppress a slight blush.

"Now tell this one thing Rainbow Dash, am I ginger?" The Doctor said as if it was the most serious thing in the world.

"No your mane is just brown." Rainbow Dash asked with her head slightly bent, "How did you not know that?"

The Doctor let out a loud melodramatic groan before answering, "Why am I never GINGER? Even as a pony I am STILL not GINGER!" The Doctor yelled, before looking at the mare in front of him,

"Sorry, new body, and there isn't a mirror in here so I have no idea what I even look like!" The Doctor said laughing.

"Hey! You are avoiding my question! Who are you!" Rainbow Dash said almost accusingly.

"Why does it matter who I am?", The Doctor said.

"Because I just hauled your flank all the way from where I found you to this hospital! That's why, now tell me who you are!" Rainbow Dash, quickly said.

"I'm the Doctor, I'm a Time Lord from the planet Gallifrey, in the constellation Kastorborous, I'm 1143 years old. The oncoming storm, bringer of darkness, destroyer of worlds. And right now, I am really hungry." The Doctor said as if it was the most obvious thing in the world.

Rainbow Dash just stared at The Doctor, then shook her head and said,

"Huh? Doctor Who!"

Author's Note

Thanks for taking the time to read my new story. It's my first so I am not expecting it to be all that great really. But as a huge Doctor Who fan, I am hoping to make it interesting. By putting my own spin on the Doctor Whooves thing. I realize the chapter ended with a bit of a cliff hanger. But I will be chugging out new chapters hopefully daily. Depending on whether or not this gets off the ground.

Chapter 2: Ponyville

"Ooh, I forgot how much I loved that", The Doctor said with a smile that rivaled Pinkie Pie's.

"What are you talking about? What's your name? Ya know what people call you!", Rainbow Dash replied obviously annoyed.

"The Doctor, call me The Doctor, my name isn't important.", The Doctor said pacing around the room.

"Oh come on, you have to have a name! Everypony has a name!", Rainbow Dash pleaded to the mysterious now stallion thing.

"Alright then, John Smith. My name is John Smith.", The Doctor said offhandedly as he inspected his tail.

"No way! Nopony's name is John Smith!", Rainbow Dash said with a touch of anger.

"Well that's your choice to believe it or not. Call me what you like, but The Doctor is what I prefer", The Doctor said with a laugh.

"Egh fine...", Rainbow Dash said in defeat, "So Doctor mind telling me what THE HAY JUST HAPPENED?!", Rainbow Dash said bursting with emotion.

"Ah, you mean the regeneration?", The Doctor said happily.

"Ah-duh! What else would I be talking about!", Rainbow Dash said with a long emphasis on the word about.

"Well you see, Ms Dash, I'm what is called a Time Lord, an ancient race of beings that inhabited the world known as Gallifrey, now we evolved with a trick. No one is quite sure how it happened, though it is speculated that prolonged exposure to the time void gave us the gift of regeneration. You see each Time Lord when they are about to die can regenerate and completely heal them self. However we don't keep the same bodies as before, we get something completely new. Though I'm not quite sure how I became a pony, that bit is a tad wonky. I believe however being in this universe has something to do with it, perhaps my DNA bounded with this worlds universe, when my TARDIS was hit by a black hole slash supernova. Any who, that's enough rambling for now, all I know for sure is that I'm a pony. And I must say it is brilliant. I mean a pony! It's fantastic!", The Doctor concluded while inspecting his hoof.

"Ehh... Ya I have literally no clue what you just said, but I'll just go along with it. So you pretty much can never die?", Rainbow Dash said obviously confused.

"Oh no, of course not! Regeneration isn't always fool proof, sometimes it fails. For example if I'm undergoing regeneration and something interrupts it, I die for good. Or if I'm so badly injured regeneration can't kick in. That's why I kept thinking it was pointless you'd save me when you found me. I figured it was too late for me to regenerate. Glad to see I wrong though!", The Doctor said gleefully.

"Ah, huh. Now one last question before I take you to see my friend Twilight Sparkle. You said you were 1134 years old! How is that possible?", Rainbow Dash shouted,

"Like I said Time Lords can live for a very long time... I'm very old, sometimes I wonder if I'm too old... ", The Doctor said in thought, "In any case, you said you wanted me to meet this Twilight Sparkle?", The Doctor continued making a gesture to the door.

"Oh ya, come on she is probably still in the library, hopefully she hasn't gone back to Canterlot yet!" Rainbow Dash, said with haste.

"Canterlot? Strange that name is similar to the old Briton legend of King Arthur, his castle was Camelot... Strange.." The Doctor said slowly.

"Huh, what is a Briton, and who's King Arthur, and where's Camelot?", Rainbow Dash said obviously confused.

"Huh? Oh nothing forget about it. Alright then, lead the way, to Twilight Sparkle. !", The Doctor said enthusiastically.

Rainbow Dash and The Doctor were trotting through Ponyville, The Doctor asked several questions involving the town and pony culture. Rainbow Dash answered them as best she could but kept saying just ask Twilight she knows more than I do, The Doctor still was very impressed with the town saying the words "Fantastic!" and "Oh, well that's brilliant!", to describe most of Ponyville. Then when they got to the library Rainbow Dash she had to talk to Twilight alone for 10 minutes.

"Oh it's fine, I understand go be with your friend!", The Doctor said happily.

"Are you sure you'll be okay on your own for 10 or so minutes?", Rainbow Dash said worry.

"Yes, I'm an ancient alien who saved the universe countless times, even created it as well... Now isn't that a story...", The Doctor said, reminiscing on his past lives.

Rainbow Dash looked at him with a you're crazy look. Before The Doctor sighed and continued, "Okay, okay, I promise I won't get into any trouble! Now go!" The Doctor said reassuring Rainbow Dash.

Rainbow Dash looked at him for a few more seconds before saying, "Ah-huh, well I better not have to save your flank again!", she said teasingly before flying into the library.

The Doctor to his credit at least tried not to get into any trouble anyway. But when he heard that scream well... How could he resist? He followed the scream to an ally where a grey Pegasus pony with a yellow mane and... Very strange eyes, was being harassed by two colts.

"Look freak! Just give us your bits! And nopony will get hurt!", the first colt warned.

"No, leave me alone!" The odd eyed Pegasus pony said, before attempting to fly away. Then flying into a wall.

Both of the colts laughed at her before the second colt continued.

"You really are just stupid aren't you? You can't even save yourself right!", The black maned colt laughed.

"Now you have one last chance to give us your bits or we are going to have to get ROUGH", the first colt said violently.

Then a third voice was heard, "Oi! Leave her alone!", The Doctor warned.

"Stay out of this! This has nothing to do with you!" The black maned colt snarled.

"Oh you'd like that wouldn't you, for me to run. What can't handle it, once you have someone your own size to pick on?" The Doctor said with anger. Before then continuing, "I'm giving you one chance walk away", The Doctor said slowly

"Who even are you anyway?!" The orange coated colt said with confusion.

"Me? Ahh well, no one special, people call me The Doctor, know why?", The Doctor said picking up a rock.

"Why?", the two colts instinctively asked.

"Because I help people.", The Doctor said as he flung the rock as a nearby scaffold which knocked over a large amount of pink paint and drenched the two colts.

"You-you're crazy!", the black maned colt panicked.

"Come on Storm, let's leave these two freaks!" The orange haired pony, quickly said before he and his friend ran off, desperately trying to shake off the paint to no avail.

"Fury of the Time Lord", The Doctor laughed to himself and rolling his eyes. Before looking at the mare that hid her face with her hooves.

"Oh no, I'm so sorry. I didn't get any paint on you did I, I'm The Doctor.", he said to which he got no response.

"I'll leave you be then.", The Doctor said, before turning to trot away. When suddenly he felt a warm embrace around his neck.

"Thank you so much, Celestia knows what they would have done to me if you hadn't come along!", the light grey pony cried while tightly holding on to her saviors neck.

"It was nothing, I couldn't let those two get away with harming such a sweet mare like yourself.", The Doctor said smiling.

"You saved me, and that was the kindest thing anyone has ever done for me. My name is Ditzy", Ditzy said still crying

The Doctor returned the hug while Ditzy cried in his arms.... Or forearms. He had a strange case if déjà vu as well... Ditzy stopped crying however she still clung to her mysterious hero. Until finally The Doctor broke the silence.

"Ditzy not so sound rude, but do you mind if you let go of me." The Doctor said obviously uncomfortable with the closeness.

"Oh ya, sorry about that." Ditzy said clearly embarrassed, trying hard to conceal her heavy blush.

"Do you think you'll be okay Ditzy?", The Doctor said warmly.

"Yes, I'll be fine. Will I be seeing you around Doctor?", Ditzy said coyly.

"It would appear so, until next time Ditzy", The Doctor said with a small blush.

The Doctor trotted off as Ditzy flew away thinking about her handsome mysterious savior... When then Rainbow Dash and a purple Pegasus slash Unicorn landed in front of The Doctor.

"Oh man, that was AWESOME!", Rainbow Dash said loudly, "You were all like, Leave her alone! And they were like who are you! And you were like I'm the Doctor, then you threw the rock, and splash! Oh man, oh man that was so cool!" Rainbow Dash, said enthusiastically while punching the air reenacting the scene.

The Doctor just laughed,"Oh come on now, it was nothing I mean I couldn't just let her be harassed by those two now could I? After all I'm The Doctor, and doctors help peop-errr ponies.", The Doctor chuckled slightly embarrassed at the sudden attention. Before remembering there was a second pony.

"Oi, I'm sorry. Where are my manners, I'm The Doctor", The Doctor said to the violet pony,

"Hello Doctor, Rainbow Dash told me all about you, I'm Twilight Sparkle, and might I say Doctor, that was quite the show of heroism!"

"Oh come on then not you too! It's what any pony would do! I was just there when it happened", The Doctor said chuckling. Before continuing.

"And also Ms.Sparkle, might I ask why you have wings and a horn?", The Doctor said curiously.

"Well you see Doctor, I'm what is called an alicorn, though I wasn't always one", Twilight Sparkle answered.

"What do you mean?", The Doctor asked.

"Well you see, I was just an ordinary unicorn until princess Celestia gave me the title of princess as well...", Twilight Sparkle, said sheepishly.

"Princess? Oh my, I do apologize Princess Twilight, I truly had no idea I was in the presence of royalty.", The Doctor said bowing before the Princess.

"Please just call me Twilight and there is no need to bow", Twilight Sparkle said while blushing slightly.

"Now Doctor if you will follow me we have much to discuss", Twilight Sparkle said as he and Rainbow Dash followed her to the library.

Author's Note

Here is the second chapter,hope you all enjoy it! "

Chapter 3: A Madman Without His Blue Box

"Of course then, lead the way.", The Doctor said while waving his hoof towards the library,

Though it was a short distance to the Library, The Doctor could have sworn it was far longer. It seemed all the pony's eyes were glued to him. Rainbow Dash must have caught it as well as she was the first to speak up.

"Ya know, is it just me or every pony staring at us?", Rainbow Dash said curiously.

"No silly, they are staring at The Doctor", Twilight Sparkle corrected, before seeing The Doctors worried face, then quickly followed up.

"Not in a bad way of course Doctor, it's just that it's not everyday we have a hero in town.", Twilight Sparkle said smiling.

"Hey! I save ponies all the time!", Rainbow Dash said slightly aggravated.

"Rainbow, last time I checked you weren't a 1000 year old alien who can get the two meanest colts in Ponyville to turn tail and run by dumping paint on them.." Twilight Sparkle, said laughing.

"Ya, I guess it was something. I'm actually surprised you stood up for Ditzy like that Doctor, not many ponies would do that.", Rainbow Dash said blankly.

"Oi well then why not? She seem's like a sweet mare to me", The Doctor asked somewhat surprised.

"It's just that, Ditzy is a bit.... Special. She has a habit of messing up a lot. And a lot of ponies don't really like her that much.", Rainbow Dash said sadly.

"And as you saw, ponies sometime like to take advantage of her because of that, I wish that was the first time someone tried to harm Ditzy. We try to help when we can, but...", Twilight Sparkle, said slowly.

"With Twilight being a Princess and all now, and me dedicating most of my time to training. We aren't around much. The rest of my friends have their own issues as well. Rarity has a huge order for dresses, Applejack is having one of the most busiest harvests in her family's history! And Fluttershy, well that pony is scared of her own shadow. She couldn't stop two colts from picking on Ditzy if she tried." Rainbow Dash, said.

"Well then luckily I'll be here for a bit, I can watch out for her.", The Doctor said looking at the sky.

"No offence to Ditzy Doctor, but she is sorta the town joke around here. It's sad. But not many ponies would stick up for her like that. So why you?", Twilight Sparkle said questioningly.

"Because outcasts need to stick by each other.", The Doctor said quietly.

"What was that?" Rainbow Dash said.

"Huh?", The Doctor said startled,"Oh, I said because it's the right thing to do!", The Doctor said with a little lie.

"I'm sure, maybe you got the hots for ol' Ditzy?" Rainbow Dash said teasingly.

The Doctor looked at her with horror before blurting out "What NO! I- Where- How-?", The Doctor stuttered with a heavy blush.

"Woah, relax there Doctor I was only teasing you, but ya know. A handsome mysterious stallion falls out of the sky. Scares away some bad colts to save a defenseless mare. I don't know Doctor, you may have to fight off some crazed mares.... It is Spring after all ya kn-", Rainbow dash said before Twilight Sparkle cut her off.

"RAINBOW! That is not something you discuss in public!", Twilight Sparkle, said sternly at her friend.

"Oi! Don't try to hide things from me! I hate that! What happens in Spring? Tell me!", The Doctor said.

Both Rainbow Dash and Twilight Sparkle blushed heavily from hearing that.

"Uh, well you don't need to know", Twilight Sparkle said stuttering.

The Doctor let out a loud and long groan. Before Rainbow Dash whispered something in his ear.

"OK! YA NEVER MIND THAT, I DID NOT WANT TO KNOW! Oi now I will have to rinse my ears with soap! I really appreciate that Ms.Dash!", The Doctor said horrified.

"Oh ya and about that, stop calling me Ms.Dash, call me Rainbow, Ms.Dash sounds way to formal", Rainbow Dash said shaking her head.

"Sorry, about that... Em Rainbow", The Doctor said shyly.

"Okay we're here!", Twilight said joyfully at her old home.

"Ya know normally I hate libraries but this isn't all that bad.", The Doctor said looking around.

"What?! How can you hate libraries! They are magnificent!", Twilight Sparkle said horrified.

The Doctor cringed at the words, he knew all too well why he despised libraries. A day where he lost one of his closest friends, where innocent archaeologists were devoured in seconds... And... The day he met and lost his wife. Where he had to look helplessly on while handcuffed to a pole as his wife died before his very eyes.

The Doctor stuttered, before telling a lie, "Oh, I just um. Never been a big fan of reading is all", The Doctor said trailing on his words.

"How can you not like reading!", Twilight Sparkle said still shocked.

"Twilight, I'm a time traveler, when you have literally the entire universe to explore, at every point in history, why bother reading.", The Doctor said.

"Because reading can take you to whole new worlds! You can be an adventurer in the jungles or yo-" Twilight Sparkle said before being cut off.

"A la la la la. I'm going to stop you right there, I can go to every planet in the universe, at every point in time. I can watch the birth and end of entire civilizations, 1000's of years for one, and minutes for me. And I can certainly be an adventurer in the jungle, have been in fact, but that's not important." The Doctor said this time truthfully.

"Egh, fine but reading is still good!" Twilight said defeated.

"Geez Doctor, this is the first time I've ever seen Twilight give up an argument about reading, you're just full of surprises aren't you?" Rainbow Dash said with a raised eye brow.

When they got to a table in the library Twilight asked her assistant dragon Spike, to make some tea.

"Oh that's brilliant! A dragon! Haven't seen a dragon in ages. Hello! I'm The Doctor!", The Doctor said smiling Spike.

"Hey, Doctor, I'm Spike!" Spike said shaking The Doctors hoof.

"Now then." Twilight Sparkle said, "Tell me everything.", Twilight said sipping her tea.

"Well this may take a while", The Doctor said scratching his ear.

"I have plenty of time, go on Doctor", Twilight said warmly. A mark of a true leader The Doctor thought...

"Yes well, you see, I am what is called a Time Lord. An ancient race of humanoid beings. Do you know of Humans?", The Doctor asked.

"That we do Doctor, it is what I originally thought you were. I read about Humans once they were, an old legend from a book I read about pre-historic Equestria. It is what I originally thought you were, until I learned of your two hearts.", Twilight said.

"Yes well, we look similar to that of a Human, in fact many species do, because of how they evolved. Anyway, yes we do have two hearts which caused us to age at a much slower rate. I am 1134 years old. Granted I am an old Time Lord. But some are older than me. Technically without any dangers, a Time Lord can live for thousands of years it takes a Time Lord centuries to grow old. Almost 500 years. In some cases, before they have to regenerate. And even then we have a cycle of 13 regeneration's. Usually, but with my circumstances I may have more than 13." The Doctor said.

"If you do no mind me asking Doctor what regeneration are you on?" Twilight Sparkle said with interest.

"Well that's a good question. As of now I am on 14." The Doctor said plainly.

Twilight Sparkle nearly spit out her tea from hearing this, "You died 14 times?!" She said in utter shock, "You said a Time Lord at most can live 500 years in one life! How are you on 14, and only be 1134?" She said still dumb founded.

"I have a habit of getting into trouble, from jump starting the universe, to dying simply of old age, to falling from a building... You don't save the universe countless time without getting a few scars", The Doctor said.

"Except those scars, are dying!", Twilight Sparkle still said baffled.

"Ah well, you can't look at life that way, I don't know how many regenerations the void will grant me. Usually its 13. But that's when there were millions of Time Lords..." The Doctor said slowly.

"What happened to the Time Lords Doctor?" Twilight Sparkle asked.

"I don't really like to talk about it, but they're gone... All of them, they're all gone. I'm... I'm the last of my kind", The Doctor said emotionally.

The Doctor was looking down at his cup of tea, he was so very old. And it never really occurred to him, when he is gone, that is the end of the Time Lords. He was still looking down at his tea, so he did not notice Twilight get up. She walked over to the lonely Time Lord. The Doctor then felt a warm embrace. He looked up and saw Twilight wrapped her forearms around his neck.

"You aren't alone anymore Doctor.", she looked at Rainbow Dash who nodded in agreement. And looked sadly at the floor.

"I.. I appreciate that Twilight" The Doctor said smiling slightly.

Twilight released The Doctor and sat back down. She continued asking The Doctor simple questions such as how he traveled through Time and Space, questions about The Doctor's universe. Until finally she got around to asking him about where his TARDIS was.

"So Doctor, where exactly is your TARDIS?" Twilight asked.

"I... I don't know, I woke up in a field where Rainbow Dash found me.", The Doctor said.

"Well there definitely wasn't a blue box where you were. Just you lying in a bed of flowers in a scary pool of blood", Rainbow Dash said shuttering.

"Hmm, well looks like I am a madman without his blue box... And without my TARDIS I'm trapped in this universe...", The Doctor said slowly.

"Do not fear Doctor, I will inform the Royal Guards to go look for your TARDIS, can't be all that hard to find a big blue box. Until then have you thought of where you will be staying?", Twilight Sparkle asked.

"No, I guess I never really thought about that. I sorta supposed I be out of here before night... I guess that isn't going to happen now is it", The Doctor said looking down.

"Well your welcome to crash at my place!", Rainbow Dash said.

But before The Doctor could respond, Twilight Sparkle spoke, "Rainbow you know he can't be on a cloud he isn't a Pegasus like you."

"What, your home is on a cloud?", The Doctor asked surprised at learning this fact.

"Ya, it's huge too, and Twilight isn't there a spell you can use that can let earth ponies be on clouds?", Rainbow Dash asked.

"Well yes, there is. But even if I did it, he still can't get up there. He is still wingless." Twilight Sparkle said correcting Rainbow.

"I can carry him no problem, he isn't a particularly large stallion, I should be able to fly him up there no problem!", Rainbow Dash said enthusiastically.

"Well that would mean he would have to stay up there 24/7 unless you plan on carrying him up and down every time he wants to go back to Ponyville.", Twilight Sparkle said.

"I fear she is right, Rainbow Dash, however I would like to be on a cloud. That would be brilliant! Could you do the spell anyway?", The Doctor asked.

"I suppose I could and for your sleeping arrangements you could stay here, I don't live here anymore now that I moved to Canterlot. Now stand still so I can do the spell.", Twilight Sparkle said.

She touched her horn on The Doctor when a purple aura surrounded The Doctors body before dissipating.

"There" Twilight Sparkle said exhausted, "That should do it, whew, that took a lot out of me. I better get going now, Spike come on we're heading back to the castle. Rainbow tell every one I said hi!" Twilight Sparkle said before she and Spike walked out of the library.

"Okay bye Twilight!" Both The Doctor and Rainbow Dash said.

"Now what was that you wanting to go on a cloud?", Rainbow Dash said turning to The Doctor and giving a sly smile.

"Oh not now, right now, as you may remember me saying back at the hospital I'm am extremely hungry." The Doctor said chuckling.

"Alright, here I'll take you to The Sugarcube Corner. I'm sure Pinkie is dying to meet you", Rainbow Dash said with an all knowing grin.

"Who's Pinkie?", The Doctor asked.

"Well her name is Pinkie Pie, and she is a pony that you are bound to meet eventually and she is one of my best friends so let's go!" Rainbow Dash said before waving for The Doctor to follow her.

The Doctor and Rainbow Dash made the trip to The Sugarcube Corner and when they got there a pink maned and coated pony as her name would suggest was baking a cake when she saw Rainbow Dash and the mysterious stallion she bolted to Rainbow Dash hugging her.

"Dashie!!! I haven't seen you in like forever, well it wasn't like forever it was like a few hours ago but I'M SO GLAD your here! EEE!" Pinkie Pie squealed jumping up and down in a way The Doctor could have sworn resembled a jack hammer.

"OOOO, and who's this PONY! I never seen you before and I know every pony in Ponyville! Which means you must be new and if you new!' She then gasped, and bolted out the door.

"What was that?!" The Doctor said picking his jaw up from the floor.

"Pinkie Pie", Rainbow Dash simply answered,

"I like her", The Doctor said grinning. "But why did she run off, did I do something wrong?", The Doctor asked.

"No, it isn't that she doesn't like you. Well you'll find out why she ran out soon enough", Rainbow Dash said laughing.

"Mrs.Cake, do you mind getting us a dozen cookies for the road", Rainbow Dash asked the pony that was working the cashier.

"Of course, dear.", Mrs.Cake answered, when she went to put the cookies in the bag. She asked, "And who's your friend Rainbow?".

"Hi, I'm The Doctor brand new. How are you?", The Doctor asked extending his hoof for a hoofshake.

"Ooh, such a gentlecolt, I'm Mrs.Cake sweetie.", Mrs. Cake replied shaking The Doctors hoof.

"Here ya go Rainbow that will be three bits.", Mrs. Colt said handing the cookies to Rainbow Dash.

"Thanks Mrs. Cake and here ya go." Rainbow Dash said handing the three bits to Mrs.Cake.

"Bye Rainbow and bye Doctor", Mrs.Cake Said waving goodbye to Rainbow Dash and The Doctor.

"Bye!", both Rainbow and The Doctor said.

The Doctor and Rainbow Dash then walked out of the Sugarcube Corner and walked down the street eating the cookies. Before The Doctor broke the silence.

"Ya know Rainbow... I never really did thank you properly for saving my life. If you hadn't gotten me medical attention then I would have died for good, in that meadow... I owe you my life. ", The Doctor said sheepishly.

"Ahh it was nothing, saving ponies is what I do!", Rainbow Dash said waving it off.

The Doctor laughed, remembering all the times he's said that to the people he saved.

"Now lets get back to the library. There is something you should see", Rainbow Dash said with that all knowing grin again.

The Doctor eye balled her but let it slide. He liked Rainbow Dash she reminded him a lot of one of his past companions.

The Doctor, and Rainbow Dash were walking to the library when Rainbow Dash asked The Doctor a question.

"Doctor, why do you travel alone, I mean it has to get pretty lonely time traveling through space and time like you do. Why do you do it alone?", Rainbow Dash said curiously.

"Well I don't go alone, usually I have companions with me..." The Doctors voice trailed off.

"What happened to them?", Rainbow Dash asked.

"... Well... Some..." The Doctor took a breath before continuing.

"Some left me.... Some, well some got left behind.... And some... Not many but some... Some died.", The Doctor said shamefully.

"Oh... I'm sorry, I figured you just... Well I don't know what I thought", Rainbow Dash said sadly.

"It's not something I'm proud of believe me. In the end I'm always alone I suppose, and it's better that way. No one or pony for that matter can get hurt." The Doctor said looking down.

The rest of the trip back to the library was met with silence. They reached the library shortly however but Rainbow then remembered the door when they heard a deafening shout.

"SURPRISE!", A huge group of ponies shouted, as The Doctor and Rainbow Dash walked in.

The Doctor shouted, as Rainbow Dash just laughed remembering all the times Pinkie Pie thrown Welcome-to-Ponyville-parties.

"Oi! Give an old pony a heart attack I can't take many more surprises!", The Doctor said laughing. They got him good. Then Pinkie Pie came bouncing up to him.

"Oh its you! The brilliant pony that bolted off when I tried to say hi.", The Doctor said smiling.

"Ya sorry about that, I saw you and I was like huh I never seen this pony before in town. Which means you had to be new, and if you were new that means no pony knew who you were and I was like *GASP*, and I bolted and invited every pony to the welcome-to-Ponyville SURPRISE PARTY", Pinkie Pie said squealing and jumping up.

"Well it's FANTASTIC, Pinkie, I'm the Doctor by the way, your friend Rainbow Dash told me all about you.", The Doctor said smiling.

"Hi Doctor! That's a funny name, but I suppose being a Time Lord from the planet Gallifrey means you get to have pretty strange names huh!", Pinkie Pie said beaming with joy, before she saw something that caught her eye and she bounced off.

"What." The Doctor said picking his jaw off the floor again.

"What." The Doctor repeated, "What!", The Doctor said getting louder. "WHAT!", The Doctor shouted.

"Ya Pinkie Pie, she's so random.", Rainbow Said looking at the pink maned pony running about.

"But, how could she possibly know all that?!", The Doctor said still not moving.

"Don't question Pinkie Pie, just roll with it.", Rainbow Dash warned.

"I can't, but, I", The Doctor stuttered.

"Just don't even try Doctor", Rainbow Dash warned again.

When then Rainbow Dash saw her other three best friends.

"Hey guys! I want you to meet The Doctor, he isn't from around here.", Rainbow Dash said.

" 'Ell howdy there Doctor! Ah' name is Applejack!" Applejack, said shaking The Doctors hoof which nearly dislocated it

" Well hello darling, my name is Rarity it's a pleasure to meet you", Rarity said, shaking The Doctors other hoof as he still couldn't really move his right one.

"Hi", a yellow coated pony said to The Doctor.

"Oh hello there, no reason to be shy, I'm not gonna bite", The Doctor said giving a warm smile.

"Sorry... My name is Fluttershy..." Fluttershy said in a barely audible tone.

The rest of the party was quite pleasant as well. The Doctor did his ridiculous dance. That he performed at an old friends wedding. It caught quite a few laughs from the crowd and he started teaching a group of filly's who identified themselves as the Cutie Mark Crusaders it. All in all, by the end a great deal of ponies were doing what they called the "Doctor Dance". He also talked with Rarity who said she was quite savvy with clothing. He asked her if she could make him a navy blue suit with rust color stripes. She agreed and said it would be a welcome to Ponyville gift. He also talked to Applejack who gave The Doctor a new found love or apples. He laughed as he once said "I hate apples, apples are rubbish". To an old friend... And despite everything he also got quite friendly with Fluttershy after he told her the wondrous animals he met as he traveled the universe. It was going great, then a familiar pony tapped his shoulder.

"Hi Doctor" Ditzy said.

"Ditzy! I'm glad you're doing better!", The Doctor said happily.

"Oh ya, you really taught those two colts a thing. When I was flying here they saw me and turn tailed and ran!", Ditzy said laughing.

"Ha! Glad to hear they won't be bothering you anymore Ditzy, no pony should treat you like that." The Doctor said with a grin.

"Well... Honestly I'm quite used to it... A lot of ponies think I'm just an idiot who can't do anything right..." Ditzy said sadly.

This time it was The Doctor who hugged Ditzy first.

"Ditzy listen to me, you're brilliant in my eyes. And I suspect your clumsiness is just a result of your eye issue. Not because of some form of mental deformity. I think every pony has you wrong Ditzy and no one has the right to treat you like that", The Doctor said with a sly smile.

"Thank you Doctor, I.... I never really thought about it like that. I just started going along with what the names people called me.", Ditzy said hugging The Doctor back. Before The Doctor broke the hug.

"Doctor can.... Can I be your friend?, Ditzy asked sheepishly.

"Of course you can! You seem simply brilliant in my eyes. And nothing would make me happier to be called your friend", The Doctor said with a bow which got a laugh out of Ditzy and a warm smile.

"Thank you Doctor, I don't really have any friends and I'm glad I have you!" Ditzy said before hugging The Doctor then running off giggling like a little school filly.

The Doctor smiled warmly, before looking up and seeing Rainbow Dash give The Doctor a wink and a sly smile. The Doctor then blushed and started mouthing words before Rainbow Dash started laughing and talking to Fluttershy about something. The rest of the party was rather uneventful. The Doctor talked to a number of guests and was friendly as possible. It was safe to say by the end The Doctor had a lot more friends. As the party died down and ponies started to leave he got a lot of "It was such a pleasure to meet you Doctor!" or "I hope I see you again Doctor!". And he swore he caught a few hungry looks from a couple of mare as they left. And as he suspected Rainbow Dash was there laughing.

After every pony left The Doctor climbed into bed and looked out the window at the stars. Before whispering,

"I miss you all, so very much", The Doctor whispered thinking about all his past companions who were all gone.

The Doctor then drifted off to sleep.

Author's Note

Here is Chapter 3! It's a bit longer that I thought it would be. I suppose I could have split it up into two chapters. But oh well, hope you all enjoy Chapter 4 will be coming out tomorrow as usual! This one also has a bit more grammar mistakes than usual. It's rather late and I needed to get the chapter out sorry for the inconvenience.

Chapter 4: Meet Chrysalis

As dawn broke through the curtains and shined on The Doctors face, he woke up suddenly in a cold sweat. Another nightmare, as usual. The Doctor hasn't had a good nights sleep in, well he lost count a few centuries ago. It was another reoccurring nightmare, or one of them. It was when he lost his best friend to Weeping Angels. Love The Doctor knew very well to never underestimate the power of it. To sacrifice yourself just to be with the man you love. It was easily one of the darkest days in The Doctors life. Amelia Pond, the Scottish girl in the English village. The girl who waited. But he was proud of her, good on you Pond., The Doctor thought to himself as he got out of bed.

Of course there were other nightmares, some of them worse than others. The Weeping Angel nightmare was easily one of the worst. Right up there with his wife sacrificing herself to save thousands. Of course these were small fry, minor. Nothing compared to the nightmare that has haunted his dreams for nearly 400 years. Gallifrey Burning, he was somewhat used to it now. But he never got used to the faces of the children as he burned the planet. All of his nightmares weren't some fictional terror he conjured on his mind. No, they were far worse they were memories....

The Doctor let out a sigh and looked at his hoofs. He then chuckled to himself as he trotted down the steps. A whole new day, and he had no idea where to start. Twilight had given him 150 bits for food. Since he was stranded in a world with seemingly no idea to leave. So he figured, well might as well go grocery shopping.

As least this place seemed quite enough,he thought, as he started trotting to The Sugarcube Corner..He doubted anything out of the ordinary would happen to this small town. When he talked with Twilight yesterday she said the only thing that threatened pony kind currently were Changelings a devious race of shapeshifters who could impersonate any pony. They even had the nerve to attack the Princesses. But they were gone. No reason to worry about them she said. No pony had seen them in quite a while, it was assumed they ran off after they failed to take over Equestria. But The Doctor, well as brilliant as he was. He seemed to attract trouble... His mind drifted to the idea that The Changelings could attack. But he chuckled and said to himself,

"Naa, what are the chances of that happening?"

Meanwhile in Canterlot.

Twilight Sparkle woke to a new day. As she nimbly opened her eyes, she hopped out of her bed. And started to trot down to eat breakfast she saw the goddess of the sun: Princess Celestia.

"Good morning, Princess Celestia", Twilight Sparkle said as she saw down to eat a breakfast of eggs and toast.

"Twilight, please you do not need to call me Princess Celestia any more. You are a Princess as well now. Not to mention we are family by marriage.", Princess Celestia said sighing at Twilight Sparkle.

"Right I'm sorry, old habits die hard I guess.", Twilight Sparkle said chuckling nervously.

"Mmhm, so Twilight, I assume you are off to Ponyville after you eat breakfast.", Princess Celestia asked.

"Correct, The Doctor will need some help adjusting so I am going to help him.", Twilight Sparkle said realizing she never told Princess Celestia about The Doctor.

"The Doctor, Doctor who?", Princess Celestia asked. Which brought a giggle from Twilight Sparkle.

"No no, it's just The Doctor. He's just The Doctor.", Twilight Sparkle answered.

"The Doctor, just The Doctor, are you sure Twilight", Princess Celestia said with a sudden serious change in tone.

"Um, yes, he is just The Doctor, he isn't from around her-", Twilight said before being cut off.

"Twilight, this is going to sound a bit crazy, but is this Doctor a time traveler from another world.", The Princess of the sun replied in a serious tone.

"Yes, how could you possibly know any of that?", Twilight Sparkle said dumbfounded.

"It was prophesied, long ago a nameless Doctor will arrive from the sky, and save Equestria from eternal darkness. If he has arrived then an ancient evil must soon be too.", Princess Celestia answered dreadfully. Before then continuing. "If this is the same Doctor, then he is the only hope Equestria has.", Princess Celestia said slowly.

"I see", Twilight said slowly before taking a breath. "This all escalated very quickly. Do we have any idea what this evil could be", Twilight Sparkle said nervously.

"It could be anything from The Changelings to King Sombra.", Princess Celestia stated, "Or perhaps..." Princess Celestia said trailing off. Despite her having the best poker face in Equestria there was the undeniable look of fear on her face.

"What! What could be worse then a changeling attack or King Sombra!", Twilight Sparkle said nearly shouting.

"Everything, the evil is supposed to be the greatest foe or foes Equestria ever faced. It is possible out there the enemies of harmony are banding together, and are threatening to destroy all of Equestria. I must send word to The Crystal Empire at once! They must be ready for an attack by Sombra or The Changelings, or maybe something worse." Princess Celestia said before starting to write a message to Princess Cadence and Prince Shining Armor. When suddenly a Royal Guard burst into the Dining Room.

"Princess! I have urgent news! Chrysalis she was seen in Ponyville!", The Guard said trying to catch his breath.

"What! They she hasn't attacked since the wedding attack!", Twilight Sparkle gasped.

"I know Princess, but this wasn't an attack. It was an attempted foal-napping of a young filly. Chrysalis ran off before a stallion stopped it from kidnapping the filly.", The Guard said still panting.

"What would Queen Chrysalis want with a young filly?", Princess Celestia asked.

"I have no idea your highness, but it seemed intent on taking her but fortunately like I said a stallion stopped it.", The Guard answered.

"Who saved the filly?", Twilight Sparkle asked.

"A Stallion by the name of The Doctor, Princess.", The Guard replied before seeing the faces of the Princesses as they started at each other.

"Does the name have any certain meaning?", The Guard asked.

"Yes, it does. Thank you sir. Go back to the barracks and get some rest and alert the rest of the guards for a possible attack.", Princess Celestia said warmly.

"Yes Princess", The Guard said before leaving the room.

"It has already started", Princess Celestia said slowly. "I never thought it would happen to suddenly", Princess Celestia continued.

"I will get to Ponyville immediately Celestia, and I will warn The Doctor of the oncoming storm.", Twilight Sparkle said with haste before getting up and galloping out of the room.

"May the spirits watch over you Doctor.", Princess Celestia said to herself. Before then leaving herself to warn Princess Luna of the encroaching danger.

As Twilight Sparkle galloped out of the dining room she started shouting for her assistant.

"Spike! Spike! Come on we need to get to Ponyville!", Twilight Sparkle shouted.

"What, why? What's going on Twilight you seemed worried", Spike asked getting out of bed.

"Because something is coming, an ancient prophesy is coming true!", Twilight Sparkle said rushing to get her things.

"Woah slow down there Twilight, your scaring me what's going on?", Spike asked with a nervous chuckle.

"An ancient evil is encroaching to destroy all of Equestria and the only hope any of us have is The Doctor!", Twilight Sparkle said before throwing Spike on her back then galloping out of the Castle to the train station.

Ponyville one hour earlier.

The Doctor was trotting down the street looking at all the wonderful buildings. He thought to himself it looked like slightly like Nordic architecture. For breakfast he figured he would have some muffins so he decided to head down to the Sugarcube Corner that Rainbow Dash had shown him yesterday. Also to say thanks to Pinkie Pie for the wonderful party she had thrown him. When suddenly he saw Rainbow Dash flying towards him. Before she landed beside him.

"Hey how ya doing Doctor", Rainbow Dash said clutching her head.

"I'm doing great, however, you don't look you are, are you alright there Rainbow Dash?", The Doctor said raising an eyebrow at her.

"Ya, just had a bit too much to drink last night I guess, just have a head ache is all.", Rainbow Dash said still clutching her head.

"Oh, sorry about that. That's why I haven't touched alcohol in well, nearly 200 years.", The Doctor said as a matter of factly.

"200 years? Sheesh, I can't go without Applejack's Cider for almost a week.... Well ya know, maybe that is a good thing, because your crazy enough as it is. But then again, it would be a pretty funny sight to see ya plastered.", Rainbow Dash said with a devilish grin.

"Well don't get your hopes up Ms.Dash, there is a reason why I stopped drinking.", The Doctor said.

"And why is that Doctor?", Rainbow Dash asked.

"The last time I got drunk, well lets just say it got rather.... Raunchy.", The Doctor said laughing.

"Woah Doctor, I never took you for the type of stallion to get that way.", Rainbow Dash said with a raised eyebrow.

"Believe me I'm not, and it really wasn't my fault those French, well, they sure like to party.", The Doctor said with a cheeky grin.

"French?", Rainbow Dash asked, "Are those some kinda weird alien people", Rainbow Dash asked.

"Well ya, they are kinda like weird alien people. They are humans that, let's just say really like wine.", The Doctor said chuckling.

"Huh, well if they got you to get drunk, they must be some persuasive people, so tell me Doctor, did ya do it one of em", Rainbow Dash wiggling her eyebrows.

"Oi! You are definitely a cheeky one. 10 would have loved you.", The Doctor said with a raised eyebrow.

"10? Who's that?", Rainbow Dash asked.

"My 10th regeneration, he had. Well let's just say he had some serious vanity issues". The Doctor said laughingly.

"Well he sounds like a cool guy. So Doctor where are you headed?" Rainbow Dash asked.

"Sugarcube Corner, I have like a serious need for some muffins right now", The Doctor said licking his lips.

"Muffins huh? Ya muffins are pretty sweet, Ditzy loves em too Doctor ya know.", Rainbow Dash said with a sly grin.

"And what would Ditzy liking muffins have anything to do with me Rainbow?", The Doctor said with a raised eye brow.

"Oh nothing just another similarity you two have, and maybe you want to I don't know.... Taste her muffin.", Rainbow Dash said with the most devilish grin ever.

The Doctor nearly tripped and fell upon hearing that. His face became a color of red that resembled a beet and was flushed with heat.

"Rainbo-I-What!-NO!", The Doctor stuttered.

"Calm down there Doctor, I was just teasin ya" Rainbow Dash said as she slugged him in the shoulder.

"Plus, I bet what ya really want, is to taste the Rainbow, not some muffin am I right?"Rainbow Dash whispered in his ear.

The Doctor was so stunned he literally walked into a wall and hit his head of the window of The Sugarcube Corner. All Rainbow Dash did was laugh, falling on her flank and laugh. When the Doctor got up he muttered something to himself.

"What was that Doc?" Rainbow Dash asked still laughing.

"I said, Rainbow Dash you are going to kill me. For good.", The Doctor said still blushing.

"I bet I am Doc, I bet I am", Rainbow Dash said as she flicked The Doctor's face with her rainbow tail.

"Well, Geronimo.", The Doctor uttered to himself as he entered The Sugarcube Corner.

The Doctor and Rainbow Dash walked into The Sugarcube Corner and saw Pinkie eating some breakfast with Scootaloo one of the "Cutie Mark Crusaders" The Doctor met the night before.

"Hiya Scoots, what are ya doin here?", Rainbow Dash asked.

"Hey Rainbow Dash! I was just eating some breakfast with Pinkie Pie.", Scootaloo said.

"That's cool, how ya doin Pinkie", Rainbow Dash asked her friend.

"Hi Dashie! I'm doing super-rific!", Pinkie Pie said with a mouthful of Brownie.

"Oh Doctor! How was your first night in Ponyville!", Scootaloo asked The Doctor.

"It was terrific Scootaloo, this place is simply fantastic!", The Doctor beamed.

"And Pinkie, I would like to thank you for the brilliant party last night.", The Doctor directed at Pinkie Pie.

"It was no problem Doctor! Everyone deserves a welcome-to-Ponyville party!", Pinkie Pie grinned.

"Well none of the less, I very much appreciate it, by the way Pinkie, would you happen to have any muffins?", The Doctor asked.

"Of course! What kind da ya want! We got Blueberry, Raspberry, Strawberry, Plain, ya name it we got it!", Pinkie Pie said with a huge grin holding a basket of muffins that seemed to appear out of thin air.

"Blueberry, if you please.", The Doctor asked.

"No problemo! Here ya go Doctor free of charge", Pinkie Pie said handing The Doctor another basket of muffins that also appeared out of thin air...

"Why thank you Pinkie! That is two amazing gifts you've given me, I will be sure to pay you back.", The Doctor said with a nod as he bit into a muffin.

"It is no issue Doctor! And do you need anything Dashie.", Pinkie Pie asked.

"Nah, I'm good Pinkie, but I will have one of those Doc", Rainbow Dash said as she took of The Doctors muffins.

"OI!. That is my muffin! Give it back!", The Doctor whined.

"Well, if you insist."Rainbow Dash said opening her mouth with half-eaten muffin on her tongue.

"Yeh, shrue whant it Doc!", Rainbow Dash teased.

"No, I'm good you can have that muffin Rainbow." The Doctor said shuttering which brought a laugh from Scootaloo and Pinkie Pie.

Rainbow dash then swallowed the muffin, "Good cause I don't want to feed ya like a bird Doc!", Rainbow Dash said with a sly grin. Which brought a groan from The Doctor. When then the local black smith Iron Striker came in.

"Hiya Iron, what can I do for you", Mrs Cake asked.

"Oh nothing much just that sweet little filly you have over there.", The black smith said calmly.

"Excuse me!", Rainbow Dash yelled, "What did ya just say!"

"I said you give me the filly over there and nothing bad will happen", Iron Striker said still smiling creepily.

"Iron Striker what is wrong with you!" Mrs Cake said in disgust.

"Who? Oh right "Iron Striker".", the crazed pony said.

"Huh, wait, whats going on here Rainbow Dash, why does he want me?", Scootaloo asked her idol.

"I don't know Scoots but get behind me.", Rainbow Dash ordered.

"Oh you can't save her Element of Loyalty neither can you Element of Laughter or you Mrs.Cake.", Iron Striker said still utterly calm.

"What the HAY is wrong with you dude!", Rainbow Dash yelled.

"Me, nothing it's nothing personal, just for the hive.", Iron Striker itching his ear "Sorry, you ponies have such strange bodies, so furry, so itchy", the creature said still calm.

"Okay let me rephrase who the HAY are you!", Rainbow Dash said with her fighting blood coursing through her veins.

"Oh come now Element of Loyalty, we met at the wedding, oh right sorry, I was wearing a different body then. Silly me, here maybe this well help you recognize me", The Creature said laughing maliciously.

Then suddenly The Doctor saw the creature change its body into a black winged and horned creature. It had holes in its hoofs and long natty blue hair.

"Queen Chrysalis!", Pinkie and Rainbow said in unison.

"Glad to see you all still remember me, how sweet of you.", Queen Chrysalis said with a demon grin.

"Oh look at you, you beautiful, beautiful thing.", The Doctor said as he trotted up to the Queen of The Changelings.

"What! Doc what are ya doin, ya picked a HAY of a time to flirt!", Rainbow Dash yelled at The Doctor.

"Ya do ya KNOW who she is Doctor!", Pinkie Pie yelled.

"Nope, and that's good fresh starts are good. Now tell me Queen Chrysalis was it, it's a pleasure", The Doctor said with a slight bow.

"Good, someone who finally shows me some respect! Now tell me pony! Who are you!", Queen Chrysalis said looking at the brown maned pony in front of her.

"I'm the Doctor", The Doctor said simply.

"Well then Doctor, do you fear me" The Queen snarled.

"Well no not really, but I'll tell ya what though Queen Chrysalis ever heard of breath mints, oof, you can probably turn armies around with that breath alone, am I right", The Doctor said jabbing her in the side. Which made every one in the room's jaw to drop except Scootaloo who was laughing adorably.

"Like that? Finally someone who gets my humor!", The Doctor said chuckling.

"WHO ARE YOU TO DARE TOUCH ME!", The Queen yelled at The Doctor.

"I DON'T KNOW!" The Doctor said mimicking her tone.

"Ya see, I just regenerated yesterday and honestly this is the first time I met a threatening pony like yourself. And frankly I have no idea what I am doing. Sure I saved Ditzy yesterday from two colts but that was just me being a good civilian ya know. So honestly I have no idea who I really am.", The Doctor said with a sly grin.

"Am I funny, which I guess I am, thank you Scootaloo" The Doctor said winking at the filly who was standing behind Rainbow Dash. "But who am I, now that your majesty is the real question. I guess we will find out then eh? Now what is it that you want Queen Chrysalis?", The Doctor asked.

"I want that filly over there!", The Queen said with a menacing stare at the little filly.

"I'm not scared of you Queen whatever!", Scootaloo yelled.

"You should be!", Queen Chrysalis snarled.

"No, she shouldn't, but, I'll tell ya what though. You know who you should fear." The Doctor said with scary calmness.

"Who, Doctor!" The Queen barked.

"Me.", The Doctor suddenly. "You get once chance, turn tail and run, or feel the wrath of a Time Lord, your choice, your majesty", The Doctor said mocking the Queen of the Changelings.

"And why is that you pathetic little creature why should I fear and listen to you!", Queen Chrysalis barked.

"No see the real question is, do you want to find out I'm so old now... Listen Queen Chrysalis you are not touching Scootaloo do you understand? I suggest you run away very fast, because I am running out of mercy. And you do not want to see what a Time Lord like me will do when he is out of mercy.", The Doctor warned.

"Wait Doctor... Did you say Time Lord?", Queen Chrysalis said questioningly.

"I did, heard of em?", The Doctor asked.

"The legends are true then. The Doctor who made entire armies run by his very name. The Doctor who lost his world to a blaze of fire. The last of the Time Lords.", Queen Chrysalis said stunned.

"Right you are, my turn your majesty how do you know any of that, I am not from this universe.", The Doctor said in a serious tone with a raised eyebrow.

"Doctor, you of all ponies should know the Time Void works in mysterious ways.", Queen Chrysalis said with a sly grin.

"That I do, look Queen Chrysalis it truly has been a blast but you really should go now", The Doctor said blankly.

"I really wish I could sweetie, but not even for you", Queen Chrysalis said with a devilish grin.

"Don't you dare call me sweetie, never again. Do you understand me?", The Doctor snarled.

"Oh why, because your wife River Song used to call you that, come now Doctor she's ancient history.", Queen Chrysalis said with a menacing glance.

"How, how... How do you know that name...", The Doctor said stepping back.

"Like I said Doctor I know all about you" Queen Chrysalis said stepping uncomfortably close to the Doctor.

"Tell me Doctor what makes you better than me", The Queen said nuzzling against The Doctors neck. Which this time really did make every pony's jaw drop.

"If you know me then you know why", The Doctor said staring at a piece of wall over on the other side of the room.

"I really don't then, we aren't that different you and I, we could rule Equestria together. You said it yourself Doctor, you run out of mercy, and what happened last tim-", Queen Chrysalis said before being cut off by Rainbow Dash.

"Ok Queen Chrysalis I heard enough! It's time for you to either go or you get your flanked kicked back to wherever it is you came from!", Rainbow Dash snarled.

"Egh, I forgot they were here, one moment please Doctor", The Queen said before giving The Doctor a wink.

Queen Chrysalis horn then glowed and shot a bolt of magic at Pinkie, Scootaloo, Rainbow Dash, and Mrs Cake freezing them.

"Good, about time we had some privacy Doctor.", Queen Chrysalis smiled.

"Turn them back Chrysalis!", The Doctor snarled.

"Ooh, a first name basis already Doctor, and we didn't even have to go to dinner.", Queen Chrysalis said before The Doctor interrupted her.

"You turn them back now!", The Doctor said before stepping towards Queen Chrysalis. She just laughed and flashed her horn at The Doctor freezing him as well.

"Look Doctor, I'll cut it short. I know all about you, what you did to Gallifrey, to your home. We really aren't that different, I originally came for Scootaloo, but a Time Lord, and not just any Time Lord, no the infamous renegade son of Gallifrey. He will do much better then a filly. And your looks, well that's a bonus.", She said with a wink. "Join me and we can rule my hive empire to take over all of Equestria, you and me. All of the world, at our mercy. Think of the power we could share together. All of th-" The Queen said before being cut off.

The Doctor had heard enough, and gave her an answer "We are nothing alike Chrysalis, don't get me wrong I like a naughty girl. Err... Mare....But come on, you really expect me to turn around and join the dark side. Oh look at that I am a pop-culture reference type of man err stallion. Anyway, look, I can help you. But only the right way which means you turn around and stop whatever you have planned. That means no taking over Equestria. I can help you find a home that has a similar climate to that of Equestria, once I get my TARDIS back I can help you I swear.", The Doctor finished.

"Oh you mean your blue box, oh yes, did I forget to mention we have that as well. When my scouts came in and said they found a blue box that said "Police". Well I immediately knew. Anyway, shame you do not wish to join me by choice. I suppose I will just have to force you to become a Changeling and then you won't have much say in the matter.", Queen Chrysalis said with a devilish grin before her horn started to glow and she started moving it towards The Doctor.

Rainbow Dash and The Doctors eyes met for just a second. And despite Rainbow Dash being unable to move her face The Doctor saw all he needed to see. Her eyes said it all. Then The Doctor went into overdrive mode. Alright think, think. Queen bad breath over here is about to turn you into a Changeling so you can become her king or whatever. But that's very bad that is a no no. So how do you get out of this, COME ON THINK, you married a psychopathic woman before, and while she was loads of fun. This Queen Chrysalis seems like a bit naughtier then I like. Okay good, because she put half strength into her spell I can still slightly move, okay come on, COME ON, OH THAT'S IT! I'M THICK I'M OLD AND I'M THICK! HOW I LOVE YOU MUFFINS

The Doctor with all his strength moved his hoofs and grabbed the muffin basket "I'm so sorry muffins...", The Doctor said sadly. But before The Queen could respond he dunked the basket on her head. Which broke her concentration just long enough for the spell to break over Pinkie Pie and Rainbow Dash.

"OH IT'S SO ON NOW!", Rainbow Dash yelled as she flew full speed right at Queen Chrysalis side which caused her to have a loud yelp.

"It's PARTY TIME!", Pinkie Pie laughed manically. Which made even The Doctor step back a bit in fear. In anticipation of what she was about to do. Suddenly Pinkie Pie pulled out a cannon out of thin air.

How in the name of sanity does she do that?!, The Doctor thought to himself. Before then Pinkie lit the cannon and fired it at Queen Chrysalis which caused her to fly through the door with a loud Oof

Queen Chrysalis snarled out, "Fine Doctor, today you can stay a pony, but I'll be back, and YOU WILL BE MINE TIME LORD!" Before then growling and flying off.

"Scoots you okay!" Rainbow Dash said to her number one fan. And as every pony checked each other to see if they were okay. The Doctor kept looking out in the distance to where Queen Chrysalis flew off too. She gave up way to easily. She could have easily toppled the entire town if she desired. So why give up so easily? She seemed injured but not that badly. She would be back, for him or Scootaloo for reasons he didn't quite understand. But it would be different because then he would be ready. Before then Rainbow Dash came up to him.

"Yo Doc, you okay." Rainbow Dash said as she came up beside him.

"Rainbow, the psychopathic Queen of the Changelings just came on to me, and tried to get me to join her army as her king. How do you think I feel?", The Doctor said looking at Rainbow.

"Ya, that was wild, usually Changelings feed off of love. I didn't think they were capable of it. But then again she was probably in love with the idea of how much power a Time Lord or whatever could give her.' Rainbow Dash said eyeballing The Doctor.

"Either way, she said she would be back for me. And possibly Scootaloo, who exactly is Scootaloo? What is so special about that filly that would make the Queen herself come to take her, herself. It doesn't make any sense she is just a normal filly. What would she need with Scootaloo?", The Doctor asked.

"I don't know Doc, I definitely wasn't expecting that. Especially her coming on to you, now that was weird. I can't believe she thought you were going to join her!", Rainbow Dash said in disgust.

"I definitely wouldn't be a part of a rouge army of hive mind creatures. Especially be that queens husband, don't get me wrong I like a bad girl but sheesh.", The Doctor joked.

"But she will be back like you said Doc, but now we know. And we will be ready, I sent a message to Canterlot so the Princesses know what happened here. Twilight should be here soon. Until then how 'bout I buy you a few more muffins since Chrysalis made off with yours?" Rainbow Dash said hoofing The Doctor in the chest.

"Good, I am still starving" The Doctor laughed as we went back inside, with a final thought on his mind.

Why is it always the crazy ones?

Author's Note

Phew, sorry this took so long. I got very busy recently. Hopefully I can get Chapter 5 out sooner than later. Hope you all enjoyed! Stay tuned!

Chapter 5: Questions Without Answers.

Twilight Sparkle met the train ride back to Ponyville with extreme fear. This could not be happening, she thought. An ancient prophesy about a nameless Doctor, who he alone was the only hope Equestria had from eternal darkness. She pondered the strange turn of events that turned life upside down not only in the Royal Court but also in Ponyville. Queen Chrysalis herself attempting to foalnap a filly? It made no sense, what could she possibly need with a filly? And of course The Doctor was there to save the filly. After all only he could save Equestria which brought another question to light. What about the Princesses surely, Princess Celestia or Luna could stop the evil that was encroaching on Equestria. Or what about the Elements of Harmony if that could stop the God of Chaos: Discord. Why couldn't they stop this? What was so special about The Doctor that he alone could be the only hope any pony had. Questions such as this flew through Twilight Sparkle's mind. And of course no answers would be provided. Perhaps The Doctor will have some idea of what is happening. , Twilight Sparkle continued to think to herself. When suddenly the train came to a stop and she looked out the window and saw Ponyville station.

Twilight Sparkle let out a sigh, before saying to her assistant Spike, "Well, Spike we're here. Let's go find The Doctor."

Twilight and Spike left the train and as she expected a whole mass of Royal Guards were patrolling the streets. Princess Celestia must have dispatched them in light of the spotting of Queen Chrysalis, Ponyville only had about 6 guards. And there was easily two dozen Royal Guards that she could see. When then a Royal Guard came up to her.

"Princess Twilight, I am here to escort you.", The Royal Guard stated as he bowed to the Princess.

"Oh, that will not be necessary sir, I know my way around.", Twilight Sparkle said warmly to the Royal Guard.

"Apologies Princess, but Princess Celestia herself asked for you to be escorted. The facts are still blurry around the whole Queen Chrysalis mess. And right now we have to prepare for the worse.", The Royal Guard replied.

"Well, alright then, may I ask for your name?", Twilight Sparkle asked.

"Certainly Ma'am, Sergeant Turbo at your service Princess Twilight", Sergeant Turbo said with a bow of his head.

"Alright Sergeant, do you know where I can find The Doctor, I must speak to him urgently.", Twilight inquired.

"Yes Princess, he is currently at the local bakery, Sugarcube Corner.", Sergeant Turbo said.

"Right thank you, now let's be off. Come on Spike", Twilight said to her friend.

"Lead the way Twilight.", Spike said.

The Doctor sat uncomfortably his mind racing with so many questions. Why Scootaloo? What did Queen Chrysalis have planned for her? It doesn't make any sense.... There were certainly more questions than answers floating about. Fortunately Scootaloo seemed alright. She was a tough filly, she wasn't about to let Queen Chrysalis scare her. And on top of that she had a guardian someone who would protect her. And would risk his life for her. The Doctor.

The Doctor was still lost in thought when Scootaloo sat next to him.

"Hey Doctor, I wanted to thank you. For standing up for me like that. It was pretty awesome how you did that.", Scootaloo said warmly to The Doctor.

"Of course Scootaloo, I wasn't about to let Queen Bad Breath steal you!", The Doctor joked with a warm smile.

"I know, but ya know, I am kinda confused. What did she want with me?", Scootaloo asked The Doctor.

"I wish I could tell you Scootaloo, but I have absolutely no idea.", The Doctor said rubbing his chin. "But I wouldn't worry about it to much, because as long as I am here, no evil Queen is taking you away.", The Doctor said with a smile.

"Thanks Doctor, hey can I make you a fan-club too? I already have one for Rainbow Dash, how bout a Doctor fan club!", Scootaloo said enthusiastically.

"Nahh, thank you though Scootaloo, I... I appreciate it, but I don't really deserve a fan club.", The Doctor said sadly.

"Why not? You just saved me from the Queen of the Changelings and not to mention what you did for Ditzy yesterday. You're a hero Doctor!", Scootaloo asked.

"Maybe one day I will tell you Scootaloo, but for now let's hold off on making a new fan-club eh?", The Doctor said with a sly smile.

"Alright, Doctor but if you ever want one just ask okay!", Scootaloo said slightly disappointed.

"I swear if I ever want a fan-club, you will be the first to know." The Doctor said booping Scootaloo's nose.

"Will do Doctor, and thank you again for saving me", Scootaloo said hugging The Doctor's neck, which nearly shattered his two hearts to pieces.

Scootaloo then got up and went to talk to Pinkie Pie about something outside, leaving The Doctor with his thoughts once more. Though not for long, because then Rainbow Dash immediately sat down where Scootaloo did.

"Hey Doc, you okay you seem a bit dazed?", Rainbow Dash asked.

"Huh? Oh yes, I'm very much alright. Just lost in thought I suppose.", The Doctor said looking down at the table.

"Ya, I get that. Wild day huh? And it's not even over yet. I overheard your conversation with Scoot's, why so hesitant about the whole fan-club thing?", Rainbow Dash said comfortingly.

"Like I said, I don't really want to talk about it. Especially with Scootaloo her being so young and all.", The Doctor said still not looking up.

Rainbow Dash then picked The Doctor's chin up and said staring at his eyes with her deep magenta eyes before saying,

"Well good thing I'm not as young as Scoots. Now what's the matter Doc, you keep talking yourself down, when you not only showed bravery to two bad colts to save Ditzy. But also just stood up to Queen Chrysalis herself!", Rainbow Dash said sweetly.

"Rainbow, like I said this is something I'm not very keen on discussing... Ya know, did I tell you about my home world Gallifrey?", The Doctor asked the rainbow maned pony sitting next to him.

"No, not to me anyway.", Rainbow Dash said blankly before continuing, "What was it like Doc?"

"Ah well, it was magnificent. It was perfect, I mean it was truly beautiful. We used to call it the shining world of the 7 solar systems. On the continent of Wild Endeavor, between the mountains of solace and solitude. Stood shining like a gem was the Citadel of the Time Lords. A mighty glass dome encased the citadel. We were the most mighty race in the universe. Looking down at the galaxies below. Sworn, to never interfere, only to watch. The twin suns setting over the horizon, the sky burnt a magnificent shade of orange where the mountains stretched out seemingly forever. Long endless slopes of hills, where shades of red grass topped with snow shined... It was brilliant...", The Doctor said reminiscing on his glorious home world. He didn't see that not only were every pony in the room staring at him with looks of awe. That Twilight Sparkle also walked in and gave him a look of amazement as he described the wonders of the world of the Time Lords.

"Wow, Doc. It sounds amazing. What happened to Gallifrey, I mean it just sounds so perfect...", Rainbow Dash said her voice trailing off.

"Yes Doctor, what did happen to Gallifrey? It just sounds so... Awe-inspiring.", Twilight Sparkle said her eyes beaming with curiosity.

"Oh it was, it certainly was...", The Doctor replied his voice dying as he became lost in thought over his lost home world.

"Why do you keep talking about it like it's gone Doc? I mean you keep saying it was awesome", Rainbow Dash asked The Doctor with a raised eyebrow.

"It wasn't just my people, that are gone Rainbow. My entire planet is gone. A terrible war started, between my people and a race of creatures called Daleks. It was called The Last Great Time War. It was a horrid war, the Time Lords fought with tooth and nail. But Daleks are a race of warriors. Bred to exterminate everything that isn't Dalek. The Time Lords were not fighters. We were technologically advanced sure. More than any race in fact. But we didn't have the means to wage a prolonged war against the Daleks. While our technology was put towards peace and culture. The Daleks put theirs towards means to wage war. Eventually the Daleks surrounded Gallifrey. The sky trenches held for as long as they could... We fought not only for our home world or our race. But for the entire universe. Eventually the Time Lord council, decided to end the war. They put forward a plan that would bring forth the end of time itself... And I stopped it.", The Doctor said with extreme sadness.

"Wha... What did you do Doc?", Rainbow stuttered, anticipating the answer.

"I killed them. I killed them all. I burned the planet. Destroying the Daleks, and my planet. And my race. It was something I was forced to do. It was either the universe or my race. And I chose the universe..." The Doctor said his voice trailing.

"Woah Doc, that's pretty... I mean wow, to sacrifice your entire race... By why are you still alive, no offense.", Rainbow Dash asked.

"Punishment, death would be too easy. I cursed myself to live on. My race may be gone, but I refuse to let their sacrifice be in vain. I will gladly live as the last Time Lord. When I activated the weapon, I had to live. So I ran, and I've been running ever sense. Never stopping. The curse of Time Lord. And that is all I have to say about that.", The Doctor said sadly before getting up and leaving.

The Doctor left the Sugarcube Corner, with a small tear running down his cheek. Leaving Twilight Sparkle and Rainbow Dash utterly stunned with their mouths gaped open.

"Wow, he doesn't really seem like the guy who killed an entire race does he?", Twilight said looking at the door.

"No, no he doesn't...", Rainbow Dash said nodding in agreement.

"I... I feel like I should be angry at him... But I just can't.", Twilight Sparkle said still staring at the opened door.

"I know... I guess you don't live a 1000 years without seeing some stuff. But... I mean.. Woah.", Rainbow Dash said slowly.

"I mean should we go talk to him Twilight?" Rainbow Dash asked her friend.

"No... I think right now he needs to be alone..." Twilight Sparkle said finally meeting her friends gaze.

The Doctor trotted to the library where he was temporarily staying. And sat down for a minute. He was all alone... He lost not only his race, his planet, but all his friends. Everyone who traveled with him, every single one of them were gone. They were all gone. It was a thought that never left him for a minute. He closed his eyes for a rest when he started to remember when The Master, the only Time Lord left in the universe died in his arms.

The Doctor just saved the Earth, again. From his old friend turned enemy The Master. A Time Lord who went insane due to staring into the untouched rift in time and space: The Time Void. The Doctor had just defeated him when The Doctor made a decision.

"You still haven't answered the question, what happens to me?", The Master asked.

"You're my responsibility from now on, the only Time Lord left in existence." The Doctor said as a matter of factly.

"Ya, but you can't trust him!", Captain Jack Harkness an old companion of The Doctor urged him.

"Oh, no. The only safe place for him is the TARDIS", The Doctor answered Captain Jack.

"You mean.... You're just gonna... Keep me", The Master said in disbelief.

"Mhmm, if that is what I have to do.", The Doctor answered turning to Captain Jack, "It's time to change."

"Maybe... I've been wandering for too long... Now I have someone to care for..." The Doctor said warmly,

BAM

A bullet was fired, by The Masters brain washed wife. Who obviously wasn't brain washed anymore. She shot The Chest. Before The Doctor ran to The Master and held him. As Captain Jack ran to the wife.

"Put it down", Captain Jack said to the wife.

Meanwhile, The Doctor was holding The Master before saying "Come on now, I got you."

The Master let out some loud grunts of pain and started breathing heavily before saying "Always the women", he joked.

"I didn't see her.", The Doctor apologized to The Master, as Captain Jack took the gun of the wife.

The Master let out another grunt before saying, "Dying in your arms... Happy now?", he asked.

"You're not dying, don't be stupid, it's just a bullet. Just regenerate.", The Doctor reassured The Master.

"No.", The Master said in defiance.

"It's just one little bullet come on.", The Doctor pleaded to The Master.

"I guess you don't know me so well. I refuse", The Master said grinning.

"Regenerate, just regenerate.", The Doctor said starting to panic. Before then continuing "Please! PLEASE! Just regenerate! Regenerate!" The Doctor cried.

"And spend the rest of my life... Imprisoned with you?" The Master said to The Doctor.

"You've got to... Come on, it can't end like this, you and me all the things we've done..." The Doctor said to his old friend. While The Master had conflicting emotions cross his face.

"Axons, remember the Axons? And the Daleks! We're the only two left..." The Doctor said starting to cry.

"There is no one else left..." The Doctor said tears running down his cheeks.

"REGENERATE!", The Doctor begged.

The Master who was still breathing heavily let out a small chuckle "Well, how bout that... I win.", he said with a grin.

The Doctor then held his old friend in his arms staring at his eyes, as he gasped his last breath... And finally The Doctor was truly alone...

The Doctor held the last Time Lord in existence cradling him in his arms. As he rocked his friend back and forth in his arms like a mother would to her child. As The Doctor now fully started sobbing. As he shut his eyes and squinted his face before letting out a loud.

'NOOOOOOOOOOOOOO!"

The Doctor woke up in another cold sweat. That is a something he would never forget, The Last Time Lord dying in his arms, as he could do nothing to stop him. In the end The Master won... The Doctor started going into the fetal position holding himself. As tears slowly started trickling down his face. When suddenly there was a knock on the door.

"Ah, I... I, please go away.", The Doctor begged sobbing.

"Doctor? It's me, Ditzy, are you okay?", Ditzy asked sweetly.

"Ya, I'm fine... I'm fine. Is there something you need Ditzy?" The Doctor asked from the couch he was on.

"No, not really. I just came by to say Hi. And I heard sobbing, I brought muffins?", Ditzy said warmly.

"Muffins? What flavor?", The Doctor asked coyly.

"Banana, Doctor, I made them myself.", Ditzy said from outside.

"I... Come... Come on in Ditzy.", The Doctor said slowly.

"Alright.", Ditzy said slowly opening the door to find The Doctor tears streaming down his face, hunched up in a ball on the couch. When Ditzy saw this she rushed over to The Doctor.

"Doctor?! Are you alright? What's wrong?" Ditzy said worryingly.

"I... I just had a bad dream is all Ditzy, nothing to worry about.", The Doctor said with a light chuckle.

"What was it about Doctor?", Ditzy said getting up on the couch and wrapping her wing around The Doctor.

"Someone who I cared about very much passing away", The Doctor said careful to avoid details.

"Oh, I'm sorry, I lost both of my parents. A while back", Ditzy said sadly still wrapping The Doctor in her wing.

"I'm very sorry to hear that Ditzy, it must have been hard for you", The Doctor said slowly.

"Ya it was, but loss is a part of life ya know. You can't focus on that, you need to keep moving forward, the easiest way to lose sight of the future is to lose yourself in the past.", Ditzy said philosophically.

"Wow Ditzy, that was really... Really nice...", The Doctor as the tears dried on his face.

"Is there anything else wrong? I saw you kinda run out of the Sugarcube Corner when I was flying above... I decided to go home and bake you some muffins since Rainbow Dash said you really liked them. And when I came here I saw you all hunched up...", Ditzy said her voice trailing.

"I... Ditzy... I'm... I'm just tired... I'm just tired of running.", The Doctor said with extreme sadness.

"Well, what are you running from Doctor?", Ditzy asked warmly.

So The Doctor who battled demons and gods poured his heart out for the first time in his life. He told every detail to this pony kind pony who he barely even knew. As he explained the course of his life from his adventures when he was so very young. To the Last Great Time War, to his last few regeneration's, what he did to Gallifrey. How he spent almost his entire life running from death. How he just wandered aimlessly around the universe. He told her of all the companions he lost over his long life span. And Ditzy sat there holding The Doctor as he lightly sobbed as he retold the story of his life. And finally for the first time in his life. The Doctor didn't have to bear the weight of his life on his own. He had a friend, to hold it with him...

After he finished nothing was said, they just sat there in silence before Ditzy broke the silence.

"Better?", Ditzy asked sweetly.

"Better.", The Doctor answered.

Ditzy got up and they ate delicious banana muffins together. Laughing as The Doctor told Ditzy of his adventures in the TARDIS. His life despite how tragic did have some pretty funny moments. And Ditzy sat there laughing. Then Ditzy told The Doctor of her life as well. And they spent the rest of the afternoon laughing and eating muffins. The Doctor then told her of how Queen Chrysalis is swore how she would come back for him. And Ditzy laughed at The Doctor's nickname for Queen Chrysalis, Queen Bad Breath. She nearly choked when The Doctor said the Queen came on to him. And nuzzled his neck. He spoke of the majesty of Gallifrey. When finally Ditzy asked.

"Doctor... What are you going to do once you get your TARDIS back?"

"Well, same old life I guess, traveling, whole new universe to explore, new eyes, new body. Every thing it's totally new.", The Doctor beamed.

"Al-Alone Doctor?", Ditzy asked shyly.

"Well yes, I suppose.", The Doctor responded puzzled.

"Well would it be possible...", Ditzy said trailing her words.

"Be possible what?", The Doctor said obliviously.

"Would it be possible... If I could go with you?", Ditzy asked coyly.

"Ditzy... It's dangerous, I told you about how some of my friends died.... I... I would never forgive myself if you lost your life because of me...", The Doctor said.

"Doctor, you can't be alone. When you told me of your life, I noticed one thing, you can never be alone.", Ditzy said sweetly.

"And you never will have to be again.", Ditzy said as nuzzled The Doctors neck.

"I... I don't know Ditzy... Are you sure?", The Doctor asked slightly blushing.

"Positively. I always dreamed of seeing the stars.", Ditzy reassured.

"Well, if I get my TARDIS back, then I don't see why we can't see some stars." The Doctor lightly chuckled.

"Great! Oh it will be amazing Doctor!", Ditzy said enthusiastically.

"Well Ditzy... My TARDIS is currently being held by Queen Chrysalis herself. In the heart of Changeling territory. Which no pony is sure even is. It would be a dangerous journey to get my TARDIS back to begin with. And that is just the beginning...", The Doctor warned.

"I will gladly walk the road with you Doctor.", Ditzy said grinning closing her eyes. And they just saw there in silence for a moment.

When then Rainbow Dash and Twilight Sparkle opened the Door and saw Ditzy nuzzled against The Doctor, as her wing was wrapped around him. Then there was a very awkward moment where they all just stared at each other very wide eyed. Before Twilight said,

"I'm sorry, I didn't know we were interrupting something... We can come back later?"

"No!, Nope I was just leaving, yep. Uhh.. See ya Doctor, hope you enjoyed the muffins!", Ditzy said blushing madly before scurrying up and flying out the door.

The Doctor just sat there with an intense blush on his face as he was to stunned to say anything.

"So Doc... How did Ditzy's muffin taste?", Rainbow Dash teased.

"Shut up!", The Doctor groaned.

"Shame Doc, really thought you wanted to taste the Rainbow, but ah well", Rainbow Dash grinned devilishly. "Your loss", she whispered in his ear.

"Rainbow! Stop teasing The Doctor! What he does in his own time is his business!", Twilight Sparkle scolded her friend.

"Thank you Twilight, at least some pony here isn't always assuming the worst in me!", The Doctor said staring down Rainbow Dash with his intense ocean blue eyes.

"But Doctor, does this mean you and Ditzy are a... Couple?" Twilight inquired.

The Doctor let out a loud groan "No! We are not a couple! I'm an alien who will easily out live any of you! It would never work!" The Doctor said pointing his hoof at them.

"Well technically I will live forever... Since I am an alicorn now..." Twilight corrected.

"Okay I will outlive DITZY, so no it would never work Princess!", The Doctor groaned.

"So what exactly were you doing then Doc?" Rainbow Dash asked The Doctor.

"She... She came when I was in a dark place with muffins. It was a moment of weakness. Nothing more!", The Doctor said squinting his eyes at Rainbow Dash.

"Hmm, surrreee, Doc. And where exactly are these muffins?", Rainbow Dash said cynically.

"Right there", The Doctor said blankly pointing his hoof to a basket.

"Oh, huh, guess she really did just bring muffins, ooh banana!", Rainbow Dash said with a mouthful of muffin.

"OI! STOP EATING MY MUFFINS RAINBOW DASH!", The Doctor yelled at Rainbow Dash who just stuck out her tongue at The Doctor.

"Right anyway.... The reason we came Doctor, we need to talk.", Twilight Sparkle said gazing at her friend who was gorging herself on muffins. Before she grunted and asked her friend "Rainbow, please stop gorging yourself on Muffins! This is serious!"

"What! They're Ditzy's muffins, you know how delicious these things are!", Rainbow Dash whined.

"Egh whatever, anyway Doctor we need to talk.", Twilight Sparkle said shaking her head at her friend.

"About what exactly Twilight?", The Doctor asked curiously.

"About an ancient prophesy, involving you.", Twilight Sparkle said seriously.

"Oh great, here we go again.", The Doctor groaned.

Author's Note

Annnndd that is saved for another day. Yep I know, sudden ending but. This chapter is long enough as it is. So I am splitting it into two parts, I really rather not have Chapter 5 be around 10,000 words. So I will have two chapters of about 5000 words. Hope you enjoyed Chapter 5.

Chapter 6: Goodbyes And What Not.

"So Twilight feel free to jump in at any time to correct me here. So pretty much an ancient Equestrian prophesy, for told me falling out of the sky.", The Doctor asked in disbelief.

"Yes", Twilight Sparkle said blankly.

"Right, and in that ancient Equestrian prophesy it said that I, alone am the only hope Equestria has from being being plunged into eternal darkness.", The Doctor said still giving her a glance of You're-Joking-Right?

"Yes.", Twilight Sparkle said still in the same manner.

"Okay, so this prophesy not only does not know the outcome of this "great conflict", that will take place very soon. By an evil that could range from the Changelings to an ancient evil king. Who may or may not have been defeated by you and your friends last year.", The Doctor said staring at her with his wide open ocean blue eyes.

"Pretty much...", Twilight Sparkle said with a nervous chuckle.

"Oi", The Doctor said rubbing his eyes with his hoofs. Before then continuing. "Fat lot of good that prophesy does eh? We not only do not know when this "evil" will descend upon pony kind and pretty much the entire world. But we also do not have a blasted clue on who or what is descending.... I suppose attack of the bunnies is a bit too optimistic then?", The Doctor said dryly.

"I'm afraid so Doctor, what ever this evil is. It is apparently the greatest foe, the forces of harmony have ever seen. And apparently the Elements of Harmony or the magic of The Princesses is not enough to stop it.", Twilight Sparkle explained.

"Oh that is simply BRILLIANT!", The Doctor said knocking books of the a table in rage.

Twilight just looked on with a face of worry. She couldn't think of anything that the magic of The Elements or The Princesses couldn't stop.

"Yo Doc! Look I don't like this anymore than you do! But there is no point in flipping out on these books!", Rainbow Dash scolded.

"I know... I know, let's just say I have a very, very.... long history with ancient prophesies. And most of them ended with the people I cared about either dying. Or getting hurt. So my apologies to the books. But right now, I could really, REALLY, just need a moment if you please, for everyone to just shut up." The Doctor said angrily, as he put his hooves on his head and went into a deep thought.

Rainbow Dash thought about getting into a screaming match with The Doctor, but he really didn't deserve it. So she just that there with her hooves crossed angrily trying to calm down. The minutes passed by like hours. As The Doctor just sat there with his eyes closed tightly, hooves in his mane as he tried to figure out the situation that now was put before him.

"Alright look, if we are going to do this, I'm going to need a couple of things. Number 1, muffins. Bring 'em all in. I don't care which flavor, though banana or blueberry wouldn't hurt... Anyway Number 2, I am going to need a map of Equestria and the surrounding lands. We need to figure out ever possible location that the hive of The Changelings could be. Because Queen Chrysalis let it slip she had my TARDIS, and no one. Ever. EVER. Touches my TARDIS. Number 3, Rainbow I need you to give me a full background of Scootaloo, Queen Chrysalis obviously wanted her for a reason. And I highly doubt it was because she has a lot of spunk....", The Doctor finished before giving a serious stare at the two ponies who sat across from him.

"Aye, aye Cap'n", Twilight Sparkle, said as she got up and started searching the Library for maps of Equestria and any possible surrounding lands.

"You got it Doc", Rainbow Dash said giving a mock salute.

"... Never do that again Rainbow. I hate that, never again. Got it? Good, let's get to work. Allons'y", The Doctor smirked as he let out a chuckle.

So The Doctor and his friends got work immediately on the task that was put fourth in front of them. Twilight Sparkle set out a lay of maps and charts of Equestria and the lands that surrounded it. And brought out a chalk board so they could narrow down a few places. And Rainbow Dash gave a summary on everything she knew about Scootaloo. How she was found as a newborn on the steps of The Sugarcube Corner. How it was just always assumed that she was orphaned off. And how she still couldn't fly. And her fighting spirit. The Doctor listened intently. As he still studied the maps set before him. As the hours past and it grew to evening, and evening grew into night. Princess Luna's night sky sparkled with the dazzling stars. But Rainbow Dash grew a bit impatient.

"UGH, Doc! Did you figure this out yet! I mean sheesh we've been here for almost 6 hours! We are almost out of chalk we have been writing and erasing so much!", Rainbow Dash whined.

"Shut up, I am being clever over here! I don't need any distr-..." The Doctor stopped talking before getting wide eyed.

"Hey don't tell me to shut up! And what! Scared to keep talking!", Rainbow Dash said squinting her eyes at The Doctor.

"QUIET! Twilight! Look over here to the south west of Ponyville these mountains what are they called! To the immediate south of the Everfree forest!", The Doctor said in a tone of utmost importance.

"Those? They are known as the Scarlet Mountains. Dragon territory.", Twilight explained perplexed.

"Dragons! Right, when was the last time dragons have been seen to the south east of Ponyville! Because if I remember correctly when you told me Spike went to go with the Dragon migration it went from south EAST to the North West! They never crossed the Scarlet Mountains, do you not find it odd these Scarlet Mountain dragons would not follow their instincts and go on The Dragon migration!", The Doctor said shaking Twilight.

"But, if they're no dragons... Then what could possibly be in lurking in the Scarlet Mountains?", Twilight Sparkle said confused and rising, while her voice raised in volume.

"Oh my LUNA! DOC! The HIVE! It's in the Scarlet Mountains isn't it!", Rainbow Dash said her enthusiasm bursting through.

"OH YES! The Changelings were seen flying South West of Canterlot after the wedding incident no? But the trail died because the only thing after Ponyville to the South West of Canterlot was the Scarlet Mountains, dragon territory. But it isn't dragon territory. No the dragons haven't been in the Scarlet Mountains for years! They haven't been on some distant island in exile, no they have been hiding in PLAIN SIGHT!", The Doctor said rushing over to the chalk board nearly shouting. Before erasing every other location before circling and underlining: Scarlet Mountains.

"It was right in our faces the entire time. Doctor you're a genius! We now know where the hive of the changelings is!", Twilight Sparkle exclaimed.

"Ya! Now we can finally take the fight to them! I say attack them when they least expect it!", Rainbow Dash said proudly her fighting blood getting the better of her.

"No, we do not fight. We give them a chance.", The Doctor said seriously.

"WHAT!", both Twilight Sparkle and Rainbow Dash yelled in unison.

"I always give them a chance. Now look tomorrow, I will go to these mountains myself. I will talk to Queen Chrysalis. Explain to her the situation that she is now in. She will give up this pointless dream. I will find her a planet where her Changelings can live in peace. Get my TARDIS fly back here. And we will be eating muffins by Friday.", The Doctor smirked in triumpth.

Both Twilight and Rainbow then burst out laughing. And when they tried to stop they just started having a giggle fit once more. It made it even worse the confused expression on The Doctors face as to why they were all laughing.

"Oh geez, Doc. I needed that. Phew, that was good. Man, We will be eating muffins by Friday", Rainbow Dash said imitating The Doctor before laughing again.

"What? Don't diss the plan. It's a brilliant plan!", The Doctor pouted.

"Doctor, not to sound rude. But that is a horrible idea. Queen Chrysalis more than likely will fully indoctrinate you into Changeling culture. And you will be forced to be part of The Hive. Sorry but that is by far the worst plan I ever heard.", Twilight Sparkle said still laughing.

"Well, good thing you two aren't coming.", The Doctor said blankly.

"Wait, hold on Doc you're serious!", Rainbow Dash said dumbfounded.

"Of course, everyone get's a chance. I will simply explain to The Queen the situation. And that I can find her a planet that she can live on in peace.", The Doctor shrugged indifferently

"Doc, you can't be serious. She will just capture you! I mean you heard what she said back at The Sugarcube Corner! I mean why not just put yourself on a silver plate while you are at it!", Rainbow Dash said still shocked.

"It's a chance I will take. She deserves a chance just like everyone else.", The Doctor seriously said.

"Doct-", Twilight Sparkle said before being cut off.

"No, listen to me right now. Both of you. I am doing this, end of story. Everyone gets one chance. First thing tomorrow, I am going to The Scarlet Mountains, I am getting my TARDIS back. If I fail, and I do not return....", The Doctor stated.

"Doc! I mean this is nuts! You're crazy!", Rainbow Dash cut in.

"I know, isn't it brilliant. Look if I don't make it back... Tell Ditzy I am sorry. And above all else. Tell her those muffins were the best muffins I ever had in my life. Got that?", The Doctor said in such a determined tone it was pointless to try and break his resolve.

"Wait, you're going alone! Oh come on Doc, there is crazy, and there is down right suicide!", Rainbow Dash yelled.

"Maybe, however I lived a long life. And it's time I stopped running.", The Doctor took a breath. "This isn't goodbye, I will be back. And I suppose if things do go south, well I'll think of something. I always do.", The Doctor smiled.

"I don't understand, why are you going alone Doctor!", Twilight Sparkle asked in total confusion.

"Because all jokes aside, I am totally aware of the incredible danger that is lurking in those mountains. And I am going alone. No questions asked. None of you are putting your life on the line for this old Time Lord. Got that?", The Doctor said with a gaze from those big eyes that pierced Twilight's and Rainbow's very soul.

"No way Doc! I am going with you no matter what!", Rainbow Dash said in defiance.

"No you're not. Look, I have done crazier things before. Trust me. In all honesty you would probably all just slow me down. And plus if I do fail. Then The Elements Of Harmony are the only hope Equestria has then.", The Doctor said.

"But the prophesy it said the elements couldn't help!", Twilight protested.

"I don't care. Prophesies are not set in stone. They are glimpses into a future. Time can be rewritten. I know this for a fact. I just hope I don't get captured by that insane Queen and become her.... Husband that would be really, really wonky.", The Doctor chuckled dryly.

"Plus, I will be fine. I have a plan already, don't worry. If I leave tomorrow, it's around a day's journey to the Scarlet Mountains. I should arrive by Thursday, grab my TARDIS, secure peace in Equestria and be back Friday.", The Doctor said with a confident smile.

"Doctor I refuse to allow you to go alone!", Twilight Sparkle said stomping her hoof.

"Princess, with all do respect I don't care. It would be absolutely the worst possible idea to have royalty venture into those mountains with me. It would attract unwanted attention. And only risk giving me up. And with all due respect Rainbow, your ego is dangerous. It's writing checks, your body can't cash.", The Doctor burst out laughing. While the two mares just stared at him in confusion.

"Right, no Top Gun in Equestria, whoops. Any who, I mean Rainbow, your ego would get in the way of what's important. You would probably try to throttle Queen Chrysalis first chance you get.", The Doctor said gazing at the rainbow maned pony.

"But-", The two mares said in unison.

"No but's, no maybe's, and no if's. I go alone. And that. Is. Final.", The Doctor said pronouncing the words with care.

"Anyway do you think Rarity is still up by chance?", The Doctor asked.

"Ya probably, she most likely is about to close shop what does that have to do with anything?", Twilight Sparkle asked.

"Well if I am going to drop by for a hello to the Queen of the Changelings might as well look snazzy. My suit should be done now. So I will drop by grab the suit. Prep my supplies for the journey, sleep, and be out by dawn.", The Doctor explained.

"Now if you will excuse me I have a certain fashion pony to see", The Doctor said before getting up and walking out the door.

"Twi, what are we going to do?", Rainbow Dash asked her friend.

"Well you heard him, stay here and hope for the best", Twilight Sparkle said emotionless.

"What! Not you too! We can't just leave him!", Rainbow Dash said shocked.

"He's right though Dash! I am a Princess, remember the last time a Princess got captured by Changelings!", Twilight Sparkle said gazing at her friend.

"But it's pretty much suicide! He is going to die!", Rainbow Dash protested.

"I KNOW! But if he is going on this doom driven path. We would only worsen his odds of success!", Twilight Sparkle said shouting at her friend.

Rainbow Dash looked just stunned at her friends selfishness, and without saying a word she left out the door. And flew back to her home in the clouds. Twilight meanwhile just kept thinking to her self, We can not go with him! He said it is something he must do alone. I don't know if it's pride or genuine concern for our well being. But he is right, our presence would only alert the Changelings. ......

Meanwhile The Doctor just caught Rarity in time as she was just about to close up shop.

"Rarity wait!", The Doctor shouted galloping towards the fashion pony's store.

"Oh Doctor? Darling what brings you here at such late hours?", Rarity asked The Doctor,

"My suit? Is it finished yet?", The Doctor inquired.

"Why yes, I finished it this afternoon, I was going to give it to you tomorrow, but since you are here.", Rarity replied stepping into the back of her store to grab a freshly made blue suit with rust colored stripes with a white collared shirt and red tie.

"It is wonderful Rarity, you know I never been a big fan of nostalgia but, I have to say, I missed this suit.", The Doctor said grinning.

"Nostalgia, whatever do you mean Doctor", Rarity asked curiously.

"Oh, it's complicated. Let's just say I used to wear something like this quite a bit a long time ago. And well, I missed it so.", The Doctor said his voice trailing as he gazed upon the suit.

"By chance do you have a say light brown duster type overcoat?", The Doctor asked sheepishly.

"Actually I do, give me a minute", Rarity said as she fondled through some old box's. When finally she found it before letting out a triumphant "Ahh, here it is!", she exclaimed handing the over coat to The Doctor.

"Thank you so much Rairty, how much will this cost?", The Doctor asked.

"Oh nothing Darling, consider it a gift!", Rarity said with a smile.

"Oh come on, I can't take this for free.", The Doctor protested.

"Pish posh, I am known as the Element of Generosity, Doctor. Just think of it as a late present for your welcome-to-Ponyville party.", Rarity said waving off The Doctor.

"I will not forget this Rarity...", The Doctor said slowly.

"It is no trouble at all Doctor... Are you alright?", Rarity asked in concern.

"Huh? Oh yes, fine. Just, it's been a blast Rarity. I will....", The Doctor took a breath before continuing "Goodbye.", The Doctor said simply before giving her a nod and leaving.

"Okay... Well goodbye Doctor, I look forward to seeing you tomorrow!", Rarity exclaimed.

The Doctor gave her a goodbye wave as he then started trotting back to the library.

The Doctor opened the door, and was bracing himself for an angry posse of ponies to, say they would accompany him no matter what tomorrow, but nothing. No one was there. Good, just saves me time., The Doctor thought to himself. He laid out his clothes on a table and started packing his supplies. Mainly Dried Fruit and other non-perishable items that he bought on the way back from a vendor. He put them in a saddle bag that he found lying around. And after he prepped for his journey for the next day. He climbed into bed. Saying a final word. Before falling asleep.

"It really has been a blast..."

The Doctor not shockingly had another nightmare. This one was detailed about the day he lost Rose Tyler. One of his closest friends. When she fell into the void sending her to a parallel dimension. Some one he truly loved. Granted she did come back when there was the whole incident with the Earth a bunch of other planets being stolen. But the whole clone of him really made things complicated. And The Doctor, while good with complicated things, well he wasn't good at those type of complicated things. In any case, The Doctor woke up as the sun peaked over the horizon. He walked slowly down the steps. And put on his new suit and overcoat. And looked at himself in the mirror. And nodded in approval but said one thing.

"Ya know, I do miss the bow-tie..."

He gathered the his supplies, and put on the saddle bag. He took one last glance at the library he stayed in. And left. No pony was awake yet. It was still very early. Perhaps Applejack was, but no one in Ponyville was up quite yet. Which was good, The Doctor hated goodbyes... No this isn't goodbye, I will make it. I will come back, I will show Ditzy those stars. Just... Have to make past a vast army of shape shifting malevolent creatures, and who know's what on the way to the Scarlet Mountains. Just like old times... . He started took a glance towards the general direction he was meant to go in. And started walking South West. But little did he know, a certain cyan blue coated pony was watching from the clouds above.

"I don't care if you think you have to do this alone Doc, I am comin with ya, whether you know it or not.", she grinned slyly. And started flying above The Doctor as he made his journey....

To the unknown.....

Author's Note

And the start of a whole new journey. What? This isn't a slice of life story. And this is the Doctor, he was never going to stay long. So don't get your jimmies all rustled. This one is notably smaller then the past few. Mainly due to this being a sorta prologue to the Journey to The Scarlet Mountains. Chapter 7 may or may not be out tomorrow. Depends if I am up to it. These daily chapters are exhausting. And I have been staying up till nearly 3 am writing them. But I will do it for you. Because I love you all.