An Apple A Day Keeps The Doctor Away

by kaidanXD

Rating: everyone
Tags: Cutie Mark Crusaders, Big Macintosh, Crossover, Applejack, My Little Pony: Friendship is Magic, Alternate Universe, Doctor Whooves, Granny Smith, Sad
Length: 9116

Dr Whooves at Sweet Apple Acres

The TARDIS has gone a bit wrong, leaving The Doctor stuck in Ponyville until it recalibrates, or stops smoking, either is good. But a chance encounter with Applejack gets him dragged over Sweet Apple Acres! Sounds simple enough, and even The Doctor agrees it’ll be a nice change to the usual of saving the world, after all –what could go possibly wrong?

Doctor Whooves picks up a odd distress message from a little pink filly living on a rock farm. Curious he investigates, especially when moving shadows are involved!

Published 2012-04-22 16:14:01 UTC
Last updated 2012-06-10 16:48:04 UTC

Chapter 1

Applejack had stored another bucket brimming with apples in the big red Sweet Apple Acres barn. “Phewie!” she said, wiping the sweat from her brow, she was making good progress today, partly because she enjoyed the hard physical labour, and partly because she had bet Big Mac that if she could not, he would have to wear one of Granny Smith’s bonnets. If Ah keep goin’ like this, he’ll be wearin’ one for sure! She smiled at the thought.

“Soups on Everypony!” Applejack heard Granny Smith yell from the kitchen of the farmhouse, as if in response, her stomach growled nosily. Heh, Perfect timing. She thought. Ah’ll just grab somethin real quick, and then finish collectin these apples. She trotted out of the barn, closed the door, and made her way up to the farmhouse. She did all of this without even glancing at the strange blue box that now resided at the side of the barn.

Having grabbed a bite to eat, Applejack returned to the barn to collect the buckets she was using, she was just about to open up the barn when she heard an annoyed shout. Curious, she glanced around the side of the barn where the shout had come from and she was surprised to see a tan brown stallion standing in front of a blue box.

Applejack recognised his hourglass cutie mark, but couldn’t recall his name, she was sure Pinkie could tell her, but she wasn’t around the farm.

Applejack could see something was clearly bothering him, and something had happened as his dark brown mane and tail were in a complete mess, also his jacket was all muddy and stank of smoke. “Why do you have to do this NOW?!” he shouted, his frustration clear in his voice as he pointed accusingly at the blue box, which now that Applejack focused on it, she read “Police Public Call Box” written above its windows.

Strange… Applejack pondered Ah’ve never seen that ‘ere before. She watched as he attempted to open the door on the blue box, failing, he banged on the door in anger. Smiling warmly she decided to try help out this stranger “Why howdy there!” Applejack greeted warmly “Names Applejack. What seems to be the problem?” Despite her best attempt, the stallion stood with his eyes fixed on the blue box.

A small awkward silence built as the stallion looked at the blue box, he didn’t even turn to acknowledge Applejack, instead he said “Blasted thing! I was trying to fix you, but no, you had to throw me out here.” He sighed before saying “Sorry about all this you’ve caught me at my worse, look at my jacket! And my bowtie!” he finally turned to face Applejack and smiled with wide sparkling blue eyes, he then gave a vague attempt at getting some of the mud off of him “Nice to meet you, I’m The Doctor! Now, can I borrow a bath?”

Seeing that even despite his effort, The Doctor was still more or less covered in mud “Hold on to that thought” she said trotting off to get the hose, she pointed it at The Doctor and turned it to full power.
“I don’t think that… BWAH!” The Doctor attempted to say as a stream of cold water hit him, soaking him head to hoof. The torrent was turned of and The Doctor shook himself dry, looking at his sparkling clean jacket and bowtie he said “Well, I’ll hate to admit it but that worked quite well.”

Applejack laughed and asked “How the hay did you end up that muddy in the first place?”
The Doctor smiled and spoke quickly “Well I was minding my own business after having a large lunch with Star Swirl the Bearded, when all of a sudden the TARDIS starts flashing red and smoke comes bellowing out, and the next thing I know I’m being catapulted out the door and land in the mud with a big splat! So I’m here and the door won’t open until the console recalibrates, or stops smoking either way I’m not going anywhere fast, speaking of which where am I exactly looks like a nice farm.”

The Doctor grinned at Applejacks confused face. Did he just say he had lunch with Star Swirl? Ain’t that the old wizard Twilight told me about? Impossible! He lived hundreds of years ago!
“Uh, why yes!” She said, deciding to answer his question. “This here is Sweet Apple Acres, mah family and I run it, we got the best apples in all Equestria right here!” her pride was evident in her voice as she spoke, and The Doctor took in the surrounding farm land nodding.

“Ah have to ask is this here blue box is yours?” Applejack asked, The Doctor nodded and again looked frustrated “Yes, that blue box is called The TARDIS, you will have to believe me it travels through space and time, but I can’t prove this nor can I show you inside” he grinned sheepishly. Applejack just stared blankly at The Doctor.

“That thing goes through space and time?” she asked sceptically; as she was the manifestation of Element of Honesty, she could tell that The Doctor was telling the truth, but that knowledge did not help to alleviate her confusion or intrigue.“Did Big Mac put you up to this?

“Oh no! I’ve never heard of this, um, Big Mac before” The Doctor said defensively, Applejack hummed and narrowed her eyes. Again… he’s telling the truth. She thought before asking “So if yah can travel time ah guess that makes you some kind of time traveller right?” she asked The Doctor, and he seemed to gain a little more spark in his eyes “Time Lord to be correct” he said with evident pride.

Applejack pointed at The TARDIS “So you so around in that, just visiting any where any time? Sounds like a right adventure! But ain’t cha worried you’ll change anythin?” she asked with interest, and then thought What am I sayin? Why am I even believin him! I’ve got to finish collectin them apples.

Thankfully The Doctor’s answer was short, and his expressions seemed to withdraw to a blank and solemn look “Why yes quite the adventure and I’ve mostly changed things of past and future for the better, I hope, but there are some fixed points in time that cannot be altered.” He looked around at the farm and said “This is a large farm and I only see you and that big red stallion working, I could explain further, but I bet you’re busy!”

Apple nodded “Darn right we’re busy! Ah’m collectin the apples, Bic Mac’s ploughin right now, Granny Smith is bakin, and Applebloom is with her friends doin …something” she said and thought What in tarnashun were Applebloom and her friends up to?

As if to answer her question she heard the unmistakable sound of Applebloom yelp, she looked in the direction where she heard it and saw Appleboom in mid-air with her hooves flailing wildly, The Doctor also saw this and gaped as he saw the little filly land in a mound of hay. “Was that… Applebloom?” He asked and Applejack nodded
She sighed and rolled her eyes “This should be good, come on lets go see if she’s alright.” She said and lead way to the mound of hay.

They met Big Macintosh en route, he was still wearing his plough harness “Hello, I’m The Doctor, did you see that?” The Doctor introduced himself, and Big Mac nodded in agreement. “Eeyup”, he said, looking at Applejack and smiling knowingly; seeing this, Applejack said, “Ah know what yer thinkin, and don’t you get any ideas Big Mac! I only met The Doctor today! Do you know him?”

Applejack, Big Mac and The Doctor had made it to the mound of hay, and Applejack saw both Sweetiebelle and Scootaloo giggling as Applebloom was brushing dust and hay off of herself “Oh hay AJ! Hay Big Mac! Who’s your friend?” Applebloom said with a smile and Applejack sighed in relief and gave Applebloom a noogie “He’s The Doctor, but never mind that, thank goodness yah’ll right! What the hay were you doin anyway?”

“AJ! You're imbarrisin me!” said Applebloom, “Oh we been busy crusadin to get our cutie-marks! We made a catapult, and since our flanks were still blank, Scootaloo suggested we could be daredevils!” Applejack, Big Mac and The Doctor gaped. “Honestly Applebloom, you could have been hurt” said Applejack, rather concerned, “Can’t you Cutie Mark Crusaders do something a little less dangerous?”

The Doctor laughed, causing everypony to look at him as his laughing fit caused him to roll on the ground with a tear in his eye, as he attempted stifle his giggling, The Doctor asked “Did you just say…The Cutie Mark Crusaders, these three little fillies are The Cutie Mark Crusaders? But their so small, and they cause so much trouble!” this statement caused Applejack and Big Mac to laugh too.

“Eeyup,” Said Big Mac, and Applejack nodded in agreement, adding “Yeah, you could say these three are a whole heap of trouble!” before remembering The Doctor said earlier. Hang on, he seems to recognise the Cutie Mark Crusader name, and he’s a time traveller. Does this mean they cause even more trouble in the future? Her thought gave her concern over what kinds of trouble Applebloom and her friends would get in to so that even a Time Lord would know of them.

“Well, good to see your okay, I hope yah ant gonah use that catapult again?” Said Applejack, gaining the three fillies to pout “We promise Applejack” they said unanimously. Happy that she got a promise, she said “Right, ah gotta head back t’ work same as Big Mac here, ain’t that right Big Mac?”
“Eeyup” he agreed
“Then we best get to it, why don’t you three take The Doctor on a tour of Sweet Apple Acres?” the three fillies beamed at the suggestion
Sweetiebelle gasped, “We could be tour guides!”
“Can we?” Asked Scootaloo excitedly.
“Yeah! We could be The Cutie Mark Tour Guides!” Said Applebloom
The three hoof bumped and chorused “Cutie Mark Tour Guides!”

Applejack felt bad “Sorry Doctor, looks like ah dropped yah right in it, yah don’t mind do yah?” The three fillies were all giving The Doctor a pleading look “Oh go on then, I’m sure it’ll be fun!”
“YAY!” the three fillies chorused, bounding around The Doctor.
“Where will we start?” asked Scootaloo
“Well, I’ve seen the big red barn when I land…I mean arrived” The Doctor said smiling.
“Speakin of which that’s where ah’m headin see yah later everypony!” and Applejack left, followed by Big Mac, who caught up to her, Applebloom saw Big Mac whisper something and she could just hear Applejack say “Ah don’t know, he fell out the sky…”
“Have you been up to the farmhouse?” asked Sweetiebelle, who was taking a keen interest in The Doctors bowtie and jacket, and she asked “Did my sister make that? It looks like Rarity had a hoof in it.”

The Doctor hummed “What this old thing? Hoof stitched on Gallopfray don’t you know, and I highly doubt your sister had anything to do with it” he said, getting a confused look from the fillies. “Where the hay is Gallopfray, you ever heard of it?” asked Scootaloo quietly into Sweetiebelles ear, who shrugged.
“Why don’t we start at our clubhouse? It aint that far from here come on follow me!” said Applebloom, who bounded off, shortly followed by The Doctor, Sweetiebelle and Scootaloo.

After a quick walk, the three excited chattering and giggling fillies lead The Doctor to their club house “Oh wow! Now this is cool! He exclaimed looking at the tree house “Just you wait n see what’s inside.” Said Applebloom as they lead him in, The Doctor looked around at the walls which were covered in ideas on how to get a cutie mark, a crude yet colourful map of Equestria, and several drawings of a cyan Pegasus with “Rainbow Dash” written under or above the drawings.

The Doctor took a wander around inside the club house, Sweetiebelle stayed outside whilst Applebloom stuck by The Doctors side, who was taking great interest in everything, especially the left over Love Poison, he turned to see the Scootaloo crossing “Catapult constructors” off the “Cutie Mark to Do List” on the desk, and he came over and looked over her shoulder and scanned over the list. The Doctor mumbled “Good. You haven’t tried it yet…” Scootaloo overheard and was confused by what she heard. “Haven’t tried what exactly Doctor?” Scootaloo asked, her eyes shining “Do you know something we haven’t tried yet? You’re a Doctor you must know a lot about talents to do with medicine, can you teach us, and can you help us?”

The Doctor gave this some thought “Well…” he said putting a hoof through his mane “I’m not really a medical Doctor, but I can certainly give you one pointer, try not do anything too dangerous okay?”
Applebloom rolled her eyes “Ugh! You sound jus like mah sister.” She said “Ah know us three can cause a little trouble but we’re only doin it so we don’t have blank flanks no more.”

The Doctor chuckled “All in good time, believe me getting a cutie mark can be some work” Applebloom was suddenly ecstatic at The Doctor’s words “Hay, we’ve never asked you how you got your cutie mark of…” she paused to take a glance, as she hadn’t spotted it before now, and she was stumped at what she saw “an hour glass? What the hay does a doctor do with an hour glass?”

The Doctor gaped “Ah…” he said, he seemed unsure how to answer Applebloom’s question, Scootaloo came to stand next to Appleboom and said “Er, you do know how you got your cutie mark right?” it looked as if The Doctor was about to say something until everyponies attention was brought to the unmistakable shrill scream of Sweetiebelle.

The Doctor turned to see Sweetiebelle entering the club house looking scared and visibly shaking “Goodness Sweetiebelle! What the hay is the matter, how come you were out there so long?” Applebloom said as she went over to give her friend a comforting hug. Sweetiebelle smiled at Applebloom and said in a whisper “I thought I saw somepony, so I went to have a look and I saw…I saw…I’m not sure what I saw”
Scootaloo, in her usual manner said “What? You’re a Cutie Mark Crusader! You’re not scared of nopony, no monsters, and no ghosties!”

At the mention of “ghostie” Sweetiebelle shrank back slightly and made a small squeak, The Doctor put a hoof on her shoulder and smiled warmly “Now then” he said in a kind voice “Trust me. I’m The Doctor, and I can assure you that there are no such things as ghosts, now take your time but when you’re feeling a bit braver I’d like to see where you spotted this ghost.” Applebloom nodded in agreement to what The Doctor said, and nuzzled Sweetiebelle making her giggle.

Scootaloo pulled a face, sticking out her tongue and made an audiable “Ugh” noise, she then said “Hay, maybe we are the Cutie Mark Ghosthunters!” Applebloom liked this, and started skipping around the club house “Yeah! We ain’t afraid of no ghostie!” Sweetiebelle was encouraged by her friend’s words, although noticed The Doctor twitch and then face-hoof at what her friends said. Feeling confident, she said “Oh okay, I’ll lead the way” Scootaloo and Applebloom giggled as Sweetiebelle lead the group out of the club house.

The Doctor soon followed “Hay Ho Let’s Go!” he sang cheerfully, wandering at random staring intently at an odd device in his front hooves, which was currently buzzing and emitting an odd green glow from the top. Sweetiebelle noticed this and motioned for her friends to catch up with her ahead and said “Hay, what he has got there?” both Applebloom and Scootaloo looked at The Doctor, who was currently pointing, buzzing, and staring at his device repeatedly, seemingly unaware of the three fillies staring at him.

Finally, Sweetiebelle decided to ask “Doctor, what are you doing? What is that thing in your hooves?” At this, The Doctor suddenly became aware of the three fillies watching him “Oh sorry, but this whole area is just giving off the most weird readings…” he said, still looking at the device in his hooves “and this is my Sonic Screwdriver” he held it in front of the three fillies who looked at it curiously before he held it up in front of his face and must have pressed something, as it extended, opening the claws on it’s tip.

“Fascinating…” said the Doctor, whatever his Sonic Screwdriver was showing him, none of the Cutie Mark Crusaders could tell, Sweetiebelle was being as brave as she could. “We’re getting close” she said looking around “Funny I’m sure I saw something around here…” she walked on a bit and stood in a rounded clearing in the woods, she was beginning to feel scared again “This is the spot I saw the ghost.”

Applebloom, Scootaloo and The Doctor all stood with Sweetiebelle, the wind was still and it was oddly quiet, save the Doctor giving another wave of his Sonic Screwdriver “There’s nothing here!” Cried Scootaloo waving her front hooves in the air in frustration, The Doctor shushed her, and pointed and Scootaloo looked where he was pointing and she felt a chill run down her spine as she saw the ghost.

It looked like a white earth ponywearing a long dress covering its legs, but it seemed to glow slightly and faded once in a while to become see through. Nopony made a sound. The ghost floated over in their direction, as it drew near it could be seen it had a completely blank face. Applebloom made a slight squeak noise as it approached she looked up at The Doctor for reassurance, she noticed that his facial expressions had completely changed from the earlier excitement over his Sonic Screw Driver to one of sorrow.

“It’s alright, we are all friends here” he said calmly. Silence. The Doctor narrowed his eyes as the ghost stood in front of them “Can you hear me?” he asked, the ghost gave him a mute stare, this seemed to confirm something to The Doctor and buzzed his Sonic Screwdriver and bit by bit a face seemed to materialise “There we go, hello!” he said cheerfully. The ghost’s new face looked vaguely familiar to Applebloom, it was definitely a friendly looking face and was distinctively female, and had a warm smile too.

The ghost began to speak in a very soft quiet voice “He did it, I don’t know how but he secured the link” the ghost turned her head and a muffed, male voice was heard “We’re losing it! You don’t have much time, we have to contact Applejack before….” The ghost crackled and flickered, and faded away. For a moment no one moved, then, The Doctor was running.

The Cutie Mark Crusaders had to almost sprint to catch up with him “Hey! What in all Equestria just happened?!” Scootaloo shouted after The Doctor, who seemed to have no intention of slowing down “Don’t you see? It’s a message! And we have to get that message to Applejack right away because it looked important!” The Doctor said quickly and Applebloom was confused by his enthusiasm, still that face of the pony…she felt as if she knew her. “Doctor, why did that ghost, if that what it was, want with mah sis?” she asked, at which The Doctor laughed aloud “I have no idea!” He said.

They found Applejack just outside the red barn arguing loudly with Big Macintosh “Now don’t be a sore loser, yah lost the bet!” She said, Big Mac shook his head and replied “NNope!” Applejack gave an exasperated sigh “But ah picked all the apples Big Mac, that was the deal an you can’t wiggle your way outta it!” she said in an annoyed tone. She then heard racing hoof beats and turned to see The Doctor and The Cutie Mark Crusaders in tow at full gallop “What in tarnashun?” she asked.

“Ah Applejack; good to see you again! Sounds like you finished your work? Good, because I need you to follow these three to the club house, no time to explain but I’ll meet you there…” The Doctor said and carried on around to the TARDIS and quickly swung open the door and disappeared inside, with the door clicking shut behind him.
Applejack watched with a raised eyebrow, and then sighed before saying “Big Mac don’t yah think yah got outta this, girls what the hay was the Doctor rambling about?”

The three fillies looked at each other Appleboom tried to explain “Well we were in the club house yah see an Sweetiebelle saw a ghost…so she lead us an the Doctor to go see it an then it said sumthin about contactin you” Applejack was surprised at what she heard, she looked at Big Mac who looked puzzled. “Ah think the best thing to do is go see what’s there at the club house, don’t yah agree Big Mac?” Applejack asked him, and he nodded in agreement and said “Eeyup.”

The Cutie Mark Crusaders showed Applejack and Big Mac back to where they had spotted the ghost, as they neared, Applejack saw The Doctor already there, taking a strange devise out from the TARDIS “Huh, how did he get that here so fast?” asked Appleboom aloud, The Doctor placed the device in the centre of the clearing and turned it on and various implements extended and started moving, flashing or wheezing, he looked up at Applebloom’s question and said “Aha there you are! Oh you’ll be surprised how fast I can get it going, but there is still a lot of smoke but at least I got her moving!” he grinned at them all, the Cutie Mark Crusaders looked confused, Big Mac said nothing and gave Applejack a look.

“Er” She said, taking the hint. “So, what are you tryin to do now?” She watched as The Doctor pressed buttons on the device and seemed rather pleased “Well, should explain, sorry Sweetiebelle not a ghost, no such thing, but rather a projection from…who knows? This should hopefully tell us.” The Doctor pulled out something from his pocket and put it in the device. “There we go, the Sonic Screwdriver should amplify the signal, and we are live!” he swung a leaver that clanked into place.

The Ghost reappeared, and The Doctor was looking extremely triumphant, throwing a front hoof in the air with a “Yes!” The Ghost jumped at the noise and looked about “They’re here! How’s the link?” it asked and a voice from somewhere said “It’s perfect…absolutely perfect.” At which The Doctor scratched his chin looking slightly puzzled “Perfect up until your projection has no colour, who is that running the projection by the way?” The Ghost looked surprised and looked to one side “Well no wonder that little filly ran away! Can you fix it?” With a somewhat large amount of confidence The Doctor said “Of course I can!”

The Doctor pushed something, and The Ghost gained colour, her dress turned red and her body was the same shade of orange as Applejack, her hair turned the colour of Applebloom’s. “It can’t be! It just can’t be! But it is…” Applejack said in shock, unable to take it all in. Applebloom asked “Yah recognise her too? Ah can’t put mah hoof who it is.” The Ghost, if that’s what you would call it now, laughed and said “Oh sweet Applebloom, of course yah would recognize me, ah am your mother an yah can hear yah father behind me!”

Applebloom almost fainted “Whaaaaaaaa?” She managed, her jaw open wide, she looked up at Big Mac and Applejack, who also had similar expressions “Sis, I thought yah said they went to a better place?” The Doctor had to laugh at her question, he said “That’s actually quite accurate, all things considered, at a guess you’re in the Equuleus system because my machine here is using a lot of power right now to stabilise the projection, just be for warned...” A spark came out from the machine and The Doctor wildly pushed buttons and pulled leavers seemingly at random, he finished with a sheepish grin.

“Mom…I still can’t believe what ah’m seein with mah own two eyes! There’s so much I wanna ask yah, so much ah wanna show yah…” Applejack said with a tear in her eye, she reached out to touch her mother but her hoof went right through into thin air. “Oh Applejack I know, ah know it must have been hard an it wasn’t right the way we left yah, had we know back then what we have gotten ourselves into we wouldn’t have done what we did.” Her mother said, Applejack looked as if she was about to say some more, but her mother continued. “Please let me explain, the night of our disappearance; whilst Granny Smith looked after you, Big Mac and Applebloom, me and your father were out in the fields when suddenly we found this poor pony askin for help, something about a disaster, naturally me and your father agreed to help thinking he was a local, well turns out…he wasn’t from round these parts, an before we know it we were here helping these here pony folk with their farms. See a great disaster happened leaving then without food or supplies, we had to help, it wasn’t until later that we were told we could never go back to Equestria.”

The Doctor frowned “Wait, surely the Shadow Bolt Proclamation can get you back?” he asked, Applebloom picked up on him saying “get you back” but had no idea who the Shadow Bolt Proclamation was. “Yeah yah have to come back, yah simply have to!” she pleaded, her mother shook her head and said “Would that we could, an the Shadow Bolt whoever have decreed that every pony had to stay on planet until the agriculture of this world is back to normal, an boy howdy we’re still a long way to go to get this achieved...”

The Doctor’s mashing gave off a loud Bang! “Nonononononononono!” he shouted and the projection faded in and out, he furiously worked on it before the projection slowly returning to normal “Sorry… I’m running this on maximum; you haven’t got long until it completely gives out.” He saw them all looking at him Applejack smiled warmly “Doctor, if it weren’t for you, this would have never happened, I’m so thankful, we’re so thankful…” Big Mac agreed with an “Eeyup.”
Their mother said “Oh it’s so good to see you, and still on Sweet Apple Acres too! I’m glad you lot managed to keep the place going, encase that machine of the mad pony from the blue box fails just remember we are still here and we love you very much. One day we will make it home.”

The Doctor said “Quick the both of you get within the projection, with the last ounce of power I’ll take a snap shot that they can keep.” Miss Apple nodded and motioned for Mr Apple to stand next to her; he was taller and was a deep red with a blonde mane, he smiled warmly seeing his family and hugged Miss Apple “This is the happiest day of mah life.” He said. The Doctor worked away on his machine and the projection flashed briefly and a small piece of paper “Thank you, here you go Applejack” he said handing it over, on it showed her parents as they stood a few moments ago. “Thank you kindly Doctor.” She said with heart felt emotion.

“Got last few minutes buy the looks of things.” The Doctor said solemnly.
Mr and Miss Apple looked at each other Mr Apple said “Well farewell, so long and thanks Doctor! Look after yerselfs yah hear, don’t let work get in the way of bein with who you love, boy howdy didn’t we learn that the hard way…” he chuckled and waved with his free front hoof, the other being around Miss Apple.
“Oh I hate sayin goodbyes” Miss Apple said tearfully. “But it was so good to see you, it was good to see you have all grown up so big and strong, and Applebloom, looks like you’ve made some filly friends how nice!” She said smiling.

The projection began to falter and The Doctor let the machine run its course, obviously no reason to fight the inevitable anymore. “Good bye!” Mr and Miss Apple said, Applebloom and Applejack were crying, even the normally stone faced Big Mac was welling up “Ah don’t want you to go!” shouted Applejack, but it was too late, the projection faded showing both the apples waving until they couldn’t be seen anymore. Applejack wept at the spot where the projection was, The Doctor hit the switch on his machine and began to drag it over to the TARDIS, and was about to open the door when he was suddenly tackled to the floor by Big Mac.

“Nnope.” He said choking up slightly, looking straight into The Doctor’s eyes “You get them back ere now.” The Doctor was pinned to the floor with the full weight of Big Mac on him “Argh! I can’t, I’m sorry there is nothing else I can do, please I…can’t…breath…” Big Mac shifted his weight, keeping The Doctor where he was and The Doctor took a great intake of breath. “Thank you…” he said coughing.
“What the hay do yah think yah doin Big Mac? Shame on you!” Applejack shouted at her brother “Ah’m as angry as you are about how little time we got with our perants but we gotta let it go, most ponies don’t get a second chance like that.”

Big Mac moved away, but refused to make eye contact with anypony, and The Doctor stood up and brushed himself off, he nodded thanks to Applejack but also noticed that she too looked frustrated “Can ah have a word with you, in private?” she asked him, he nodded and took his machine again inside the TARDIS, motioning for her to follow him. She followed him in and let the door close behind her, unable to fully grasp the inside of the TARDIS, “Whoa nelly, it’s bigger…” she faltered The Doctor rolled his eyes “On the inside, yes yes heard it before, now what did you want to say?” he said matter of factly as he practically dumped the machine in a lower section to what looked like a large console built around a giant glass pillar with what appeared to have a pendulum inside.

Slightly surprised at the way he treated his equipment, Applejack asked the inevitable “Doctor, you’re a time traveller, can’t you stop this from happenin?” already she knew his answer from the sorrow filled expression on his face “It’s a fixed point in time, I’m sorry there is nothing I can do for you, it’s been a while since I’ve been in the good books of the Shadow Bolt Proclamation and I like to keep it that way, so I can’t just spirit them away, plus that would run risk of destroying the planets fragile ecosystem, and I’m not jeopardising all the work they have done there.”

Applejack sighed heavily “Ah reckoned that was what you were going to say…” she said disheartened. She was suddenly aware that The Doctor was hugging her “Oh…” she said, rather thankful of his sudden compassion. He released with a smile, he motioned around him “So, what do you think of the place?” he asked.
Applejack let the surroundings sink in; noticing various walkways off and a thought occurred “Doctor, this place is awful big for just one pony; don’t tell me yah travel all on yah own.” She asked and she saw his face said it all “Oh…” she said, suddenly understanding.

Applejack put a hoof on The Doctors shoulder “Nopony should be alone, don’t cha have family?” she asked, to which The Doctor pulled away and looked to the floor “I’m the last of the Time Lords, my home was destroyed in a great war, and I’ve been travelling through time and space ever since.” He suddenly perked up and continued “Actually, I’ve been meaning to get a new assistant, maybe you’d like to come along for a ride, a whistle stop tour of the universe!”

Applejack was shocked “Up and off, jus like that? No way no how, ah aint leavin may family, speakin of which, ah better go comfort Applebloom, and try get Big Mac to calm down, sorry Doctor but ah’m needed at Sweet Apple Acres.” she headed to the door and opened it to see Sweetiebelle and Scootaloo comforting a tearful Applebloom. Applejack welled up at the sight and closed the door of the TARDIS and made her way over “Don’t cry sis” she said comforting Applebloom.
“It’s not fair, we might not ever see em again!” cried Applebloom.

“It’s alright sis, at least we got this from The Doctor” She gave Applebloom the print out showing their parents, she looked at it and smiled. Suddenly wind was blown up, catching them all by surprise as the pegasi has said nothing about strong winds, and their attention was drawn to an odd noise coming from the TARDIS, they all looked as they noticed the light on the top was now flashing and it slowly began to fade, it completely disappeared, leaving no trace that it was there at all.

“Huh?” Said Sweetiebelle, Scootaloo was equally as confused and said “Wha?” Applejack mused. So he really can travel around in that blue box of his…
All of a sudden, memories flooded her mind, when she was in Ponyville, a few days gone, at the Gala, and even in Appleloosa; she realised she had heard that noise of the TARDIS before, but never noticed! He’s always about somewhere and ah never noticed…maybe that’s why he didn’t say goodbye
She felt a tugging and was pulled from her thoughts, she looked down to Applebloom “AJ? What jus happened?” she said. Applejack didn’t know what to say to that. “Ah ain’t sure, but one thing ah am sure, is that there is some lemonade up at the farm, race yah there!” she said galloped off. Quickly followed by Applebloom, Sweetiebelle and Scootaloo, laughing as they went.

Rock Farm Shadows

Prologue

Applejack was the first to arrive at the house “Yee har!” she cheered as she made it through the front door “Ah beat you three fillies! How do you like them apples?” she said and turned to see Sweetiebelle enter, gasping for breath “No..fair…you…have…longer…legs!” she managed as she made it further into the hallway, before collapsing. Applejack laughed, and turned to see Applebloom and Scootaloo enter through the door at the same time “Aw ah didn’t win, but at least I beat you!” said Applebloom, Scootaloo was shocked and said “What? No way! I was totally ahead of you!” Applejack rolled her eyes as the two fillies argued, until a very tempting smell wafted from the kitchen. “Mmm, smeels like Granny Smith has baked one of her famous apple pies, go on you three, go get yerself a slice!”
The three fillies looked at each other and licked their lips and cried in unisome “Yay! Apple Pie!” and ran off into the kitchen.

Applejack chuckled again and was about to join them when heard Pinkie Pie greet her from the Living Room “Hay AJ!” Applejack went into the room and gave Pinkie a quick hug, smiled and said “Well howdy Pinkie, great to see ya, what brings you up this way?”
Pinkie beamed a wide smile and said “Well my Pinkie Sense told me that ponies were feeling glum, so I brought cupcakes!” and she bounced merrily “How’s your day been Applejack?” Applejack noticed the big box of cupcakes on the living room table; she could almost smell the frosting and her stomach growled instantly.
“Those smell darn good Pinkie! Thank ya kindly” Applejack said “Mah days been pretty interesting, kinda got side tacked though when I met this fella who called himself The Doctor” at the mention of ‘The Doctor’ Pinkie Pie leapt in the air and gasped dramatically, gaining a very confused look from Applejack.

“You met the Doctor?! No way! I’m super jealous, isn’t he just like the best pony ever?!” Pinkie babbled and bounced even more energetically than before. Applejack got a hold of Pinkie and said “Whoa there nelly! Hold on Pinke, ya sayin yah know The Doctor fella?” Pinkie blank several times and was silent for a while, and then said “Well duh! I mean he is the most amazing, most terrific, most craziest pony in a box!” and Pinkie began to bounce around even more than before, then stopping instantly “Aw! But I don’t have time to tell you how I met him; I got to get back to Sugar Cube Corner, I got a big party planned and I am baking my hoofs off, you will have to remind me to tell you the story, but just don’t be mad at me okay?”

Applejack blank “huh, why would ah be mad at you?” she asked confused, and Pinkie Pie said “Well I know how you are Element of Honesty, and I may have told a teeny tiny lie…remember when I sang Giggle at the Ghostie? Well it wasn’t actually Granny Pie who told me to laugh away my fears, but the song would have sounded a bit odd if I said The Doctor instead right?”

The Doctor stared blankly at the console, watching the central pendulum move up and down with a slow rhythmic noise, he pressed various buttons and pulled a leaver that gave a ‘ding’ noise. He went back to watching the pendulum move up and down, creating the only noise in the TARDIS. Until an alarm bell rang.

“What?” he said suddenly focusing, he brought a monitor around to see what was causing it. He raised an eyebrow in surprise as he saw a little pink filly quietly sobbing alone in a old bed in what looked like a very dark and dusty attic room, the Doctor turned the volume up and heard the little filly whisper between sobs “Oh please, oh please, make it stop…some pony, any pony, help…” she began to cry again, and The Doctor didn’t understand, did the TARDIS just pick up the cries of a small filly? What he heard next though, filled him with dread “No pony believes me, but I’ve seen the shadows move…”the pink filly sobbed again, hiding under her blankets.

“I believe you” The Doctor said to himself, despite knowing the pink filly couldn’t hear him, he was suddenly an animated blur of motion, hitting various buttons and switches in quick succession before pausing in front of a leaver and said “Geronimo!” before pulling it, flinging the TARDIS towards where the pink filly lived.

It was a dark night at the Rock Farm and dust was blown up quickly as a blue light flashed eerily, just before a Blue box appeared. The Doctor opened the door, putting on his jacket as he left and looked around him. For a moment, he thought he was on a lunar landscape, the great rocky landscape spread before him, only broken by a small farm house in the middle of nowhere.

He slowly made his way up, and saw light from one of the windows and peeked in, he saw two simple earth ponies, one male, one female, and both glumly watching the fire burn in a dull simple living room that doubled as a dining room. The Doctor overheard the two ponies conversation “Well I don’t know, I’m just worried about her dear! Why can’t she just be like her sisters?” said the female pony with concern, putting a hoof on the shoulder of the male who was sitting in his armchair with a hard stern look on his face “Her and her fancy stories, shadows moving…” he said glumly shaking his head “All those things going on in her head, what we need, is a Doctor.”

Doctor Whooves beamed. That’s my cue! he thought, and quickly trotted to the door of the farm house and knocked. hard. The male pony opened the door “Can I help you sir?” he said with a bored tone as he looked blankly at the smiling stallion at the door “Hello! I’m The Doctor! And I think I can help you, or rather maybe some filly who is afraid of the shadows?” The earth pony raised an eyebrow and hummed before saying “You’re too happy for my liking, I don’t know who you are and I don’t know how you know that, but we have no problems here and I’ll like you to leave my farm. Now.” Before the Doctor could reply, the door was slammed in his face.

“Well, that was rude.” The Doctor muttered, he took out his sonic screwdriver and took a quick reading “Oh now that is interesting! Now looks like I’ll have to take a more direct approach, now I just have to speak to that filly.” He said as he ran back to the TARDIS.

_________________________________________________________________
Pinkie Pie physically shook with fear as she hid under her covers. Despite it being pitched black in the attic room, she could see movement she was sure of it, shadows moving in the darkness. She could feel them drawing closer, around the bed, she felt like screaming as something gripped the blankets, ready to yank them off, yet no sound came. Except a tiny, little, squeak.

Whatever it was that gripped her blankets suddenly retreated as a great wheezing noise filled the attic room, and a great blue light filled the darkness. Pinkie saw the shadows then, they moved very fast but she still saw them, and she clamped her eyes shut, terrified at what she saw. The blue light stopped flashing, but continued to dimly light the room.

Pinkie kept her eyes shut, she heard a door creak open. Watch out for the shadows! She thought, and wanted to yell with all her might, but only whimpered as she heard hoof fall across the wooden floor. The strange blue light showed a pony outline move across the room, and stood by the side of the bed. “You are going to have to trust me.” Said a calm male voice that Pinkie Pie didn’t recognise, making her flinch. “Shh it’s okay, I promise nothing will hurt you not whilst I’m here, now can you move?”
There was silence and Pinkie didn’t know what to do, she felt like she could trust whoever it was in her room, but he was a complete stranger, she quickly poked her head out from under the covers and saw the brown earth pony smiling at her. “Hello, I’m the Doctor!” he said.

The shadows began moving again, and the dim blue light began to darken, causing the Doctor to look around the room as the blackness crept over the room. Pinkie instantly hid under the covers and shook in terror. She buried her face in her bed and squeaked, keeping her eyes tightly shut. She then felt her bed move and opened an eye, suddenly it was getting brighter and she could make out the silhouette of the Doctor pushing the bed What is he doing? She thought.

A door creaked shut, and Pinkie heard hoof fall on metal Metal? My room doesn’t have a metal floor… Pinkie thought, and peaked through the covers again. Her eyes widened at what she saw. “This isn’t my room” she peeped, looking from her bed she took in the sight before her, she was now in a great domed room, with wires and pipes running everywhere, the walls had multiple circular lights in, illuminating all of it, and in the centre was a great tube with a suspended pendulum surrounded by screens of moving images, around it’s base there were slanted tables with, what Pinkie could see, a range of various leavers and flashing lights. “Aha, yes had to get you out of there, now, what’s your name miss?” said the Doctor.

“Pinkamania” She managed, still terrified and confused. “But mom calls me Pinkie” The Doctor smiled “Pleased to meet you Pinkie, welcome to the TARDIS, don’t mind me but I need to use the console” he said as he went up to the central pendulum and used buttons and levers on the tables set around it, creating a great variety of different noises “Now, lets see this shouldn’t…” the Doctor was interrupted by a great bang! And the whole place shook violently; the Doctor looked worried at this “No no no no no! What are they doing out there?” he said as he swung screen that now showed Pinkies room, Pinkie gasped as her room disappeared from view as it was now a great shadowy black hand. It made the TARDIS shake violently again.

“Make it stop! Please make it stop!” Pinkie cried, clinging to her bed as the place continued to shake. The Doctor carried on working around the console and growled in frustration “That’s what I’m doing, but I can’t seem to shake it off!” he said, now working faster than before, he looked up at the screen and yanked a leaver “Take that!” he shouted and a bright blue flash filled the screen and the shadows shrank back “Gotcha, now lets get out of here!” he said and used the console to set the pendulum moving which gave rhythmic huff every time it descended, the Doctor looked pleased as he pushed the screen way which no longer showed Pinkies room, only odd circles.

“And there we go, onwards and upwards!” The Doctor said smiling; he looked to Pinkie who was still on her bed “You know you can come up here and join me? I’ll even let you push a button or two, if you like.” he said, Pinkie didn’t move. “But, what about the shadows?” she asked, hugging her pillow tight. The Doctor walked down to her bed and said “Don’t be scared of the shadows Pinkie, they can’t hurt you.” This made Pinkie frown and she asked him “But Doctor, what about my family?”
The Doctors smile instantly faded. “Doctor?” she said, as he instantly turned and went back to the console.

“Doctor?” she asked again, causing the Doctor to sigh heavily “How often does your father smile?” he asked, catching Pinkie off guard, she thought before saying “He used to, but then the shadows came, and he smiled less and less until not at all.”
The Doctor hummed and worked the console, bringing the screen round again. “I thought as much, Pinkie, I’m so sorry, but your family is being controlled by that shadow in your room.” Pinkie didn’t understand what the Doctor was saying, tears filled her eyes as she said “But, you have to do something! You saved me, can’t you save them?” all she got was silence as the Doctor worked.

Pinkie got off from her bed and went to the Doctor’s side and watched him work,
She looked at the concentration on his face, and the concern in his eyes. It’s like I’m not here, I wonder how long I can pull a face before he notices… Pinkie thought, and crossed her eyes and stuck her tongue out. The Doctor tapped away on the console, and became aware of Pinkie standing next to him; he took a quick glance down at the boss-eyed filly, he attempted to turn his attention back to what he was doing, but completely broke down into tears of laughter.

Pinkie laughed too, happy she got him to smile again; he wiped a tear a way with one hoof and messed up her mane with the other. “A fillies giggle will brighten any ponies day Pinkie, remember that.” He said with a smile “Now, would you like to know how to get rid of those nasty shadows?” Pinkie gasped and beamed “Can you do it?” and he nodded enthusiastically, pointing with his hoof to one of the screens “See that? That is your home.” The farm looked uninviting, all dark and hardly a welcoming sight “Now, I have calculated if I send a pulse, that bright flash that got it to let go, should get it out of the house and away from your family.” Pinkie began bouncing around the consoles “Yay and I get my family back!” she said, the doctor smiled briefly and was suddenly before saying “Ah well, the thing is it’ll be drawn to our position when the pulse is used, meaning you are going to have to be brave. Very brave.”

Pinkie stopped bouncing, seeing how serious the Doctor had become. “Okay Dokie Loki. I’ll be brave, cross my heart, hope to fly, stick a cupcake in my eye!” she said smiling. The Doctor nodded and looked up at the screen again and said “We are in position, stay here I’m going to get the shadows to come out, don’t worry you’ll see everything on the screens up here.” he gestured, Pinkie noticed all the screens showed the farm house, she turned to see the Doctor make his way to the door,
before the Doctor went out, Pinkie said “Doctor? Be careful.” He simply nodded and went outside.

The Doctor pulled out his sonic screwdriver, and with a serious look on his face as he stared at the farm house shouted “Alright, funs over! You have terrified this family for too long, go on grab your coat and get outta here!” A great rumble made the Doctors eyes go wide as a great shadow rose out from the farm house. It swelled in size, filling the landscape in long shadows, spreading its hold on the landscape. The Doctor froze mouth agape. He dropped his sonic screwdriver.

“Oh no, quick do something Doctor!” Cried Pinkie at the screen, seeing the shadows fill the screen, she saw him drop something “I’ve got to do something, I bet whatever he was holding would set that pulse thing he was talking about, but I can’t go out there the shadows will get me!” she said to herself, watching the shadows move closer and closer to the Doctor. “No! I said I would be brave, Doctor look out!” she cried running for the door.

The Doctor couldn’t move, he saw the looming shadows come closer and still couldn’t do anything. Fear gripped him, if only he could get his sonic screw driver that now only lay a short distance away on the ground. The TARDIS door was flung open and the Doctor could only move his eyes to see a pink blur fly out and land beside him Pinkie?! He thought, unable to say anything as she picked up his sonic screwdriver “How the hay do you work this thing? Aha!” she said holding it between her hoofs and pushing a button on the side.

Suddenly a mass of confetti was thrown out of the TARDIS along with balloons and streamers, followed shortly by cupcakes, muffins and other baked treats. A custard pie hit the Doctor with an audible splat! Causing Pinkie to laugh out loud, louder than she had ever done before. The shadows instantly shrank back, and the Doctor could move again. “Pinkie! You did it you released its hold on me, now can I have my sonic screwdriver back please?” he asked as Pinkie continued to laugh “Ssure!” she managed before falling to the floor in continued fits of laughter.

The Doctor took his sonic screwdriver “Now that you have been weakened, and I know for a fact that you are only interested in harming ponies, you leave me no choice.” He held up the sonic screwdriver and pressed a different button, causing the TARDIS to emit a blinding white light and made the shadows fade out entirely. The Doctor wiped his face with a hanky, and noticed Pinkie had calmed down form her laughing fit “Is it gone now?” she asked, and the Doctor nodded “Oh thank you thank you thank you!” she said hugging him tight, and she looked around at all the stuff on that had come out of the TARDIS “Hay, there is enough stuff here to throw a party! I can throw one in the old silo, we can celebrate getting rid of that mean shadow, and I’ll invite my family and you of course!” she said happily.

The Doctor smiled “I’d like that, but wouldn’t you first like me to put your bed back in your room?” he said, Pinkie was too busy picking balloons up to fully hear him “Huh? Oh yeah, meet me in the old silo after!” she said and sped off, Leaving the Doctor coughing from the dust she kicked up.
The Doctor went back into the TARDIS and went straight to the console and moved the screen around and flipped a switch that displayed a count down timer. “Okay, got to get this right, otherwise she won’t see it…” he said moving leavers and pressing buttons on the console.

Pinkie had managed to set everything in place in the old silo, ready for the party, she then ran back out side, and saw she had picked everything up; she went to where the TARDIS was, and found it was no longer there. She then noticed a small piece of paper, opening it she found a note written inside:-

Dear Pinkie Pie

So sorry I had to leave on short notice, however a major event is about to occur, I leave this as a thank you for your help, and if I ever get the pleasure of meeting you again, you are a warmly welcome assistant anytime aboard the TARDIS.

Keep smiling
Doctor
P.S
Look up!

Pinkie smiled at the note, but the end confused her, so she looked up to the sky.

BOOM!

A magnificent rainbow exploded across the sky, blowing the note away from Pinkie and completely messing up her hair. She began to smile and watched the rainbow tear across the sky. In that moment she felt happy, and she wanted to share that happiness with every pony she could meet.