Doctor Whoof: Time of the Hourglass

by Muleicous

Rating: everyone
Tags: Doctor Whooves, Apple Bloom, My Little Pony: Friendship is Magic, Comedy, Other, Mare Do Well, Adventure, Derpy Hooves
Length: 14475

The Doctor meets a strange pony with a smiliar cutiemark, and help her fight a time flux

(The sequel to Doctor Whoof: Day of Discord.)
Things have quieted down in Equestria since The Doctor and his companions faced Discord and Blackspine. However, their break is interupted when a strange pegasus arrives in Ponyville looking for the time colt. Even stranger, Equestria's former first hero has begun acting very out of character.

Who is this strange pony? Why is the Mysterious Mare-Do-Well acting so strangely? Find out in the second enstalment of Doctor Whoof! ( The Story continues in The Iron Horse. Also click here to read Discord in Time! A side story to my Doctor Whoof series.)

Published 2012-01-07 12:36:33 UTC
Last updated 2012-02-09 05:08:21 UTC

Prologue

Prologue

Two months after The Doctor’s arrival...

Derpy Hooves soared out of the post office with a huge smile on her face, today was the last day of the work week and that meant it was time to visit him! The grey pegasus sped through the clouds and straight down to the roofs of Ponyville, then flew to the edge of the town and the gate of Sweet Apple Acres. It felt like it had been years since she had seen Apple Bloom, but the longer it seemed the more vivid the picture of the excited filly became. As Derpy exited the groove of apple trees, the pegasus landed with a soft thud and trotted to the farm house.

“Hello!” she said, knocking on the screen door, “Apple Bloom! It’s time! We gotta get going if we wanna make it to the blue box before night time!”

The sounds of grunts came from the barn as Big Macintosh unhooked himself from the plow. The colt walked toward Derpy and nodded politely as he passed, “Ma’am.” He said as he approached the grey pegasus.

“Hi Big Mac,” Derpy answered, “have you seen Apple Bloom?”

The farm colt nodded, “Eeyup, she was behind the barn tryin’ to fill a basket with apples.”

“Thanks Mac!” the pegasus smiled as she raced by him.

“Say hello to that Doctor fella for me, and thank ya.” Big Macintosh walked into the Apple Family home and shook his head, he had never seen a couple of ponies so excited since Pinkie Pie’s last birthday party. He figured The Doctor must be a very exciting colt to be friends with.

***

“Let’s see...” Apple Bloom said as she walked next to Derpy, her saddle bags filled with apples for the two of them to share with the time colt, “big ones, little ones, green ones, red ones, yellow ones... You’re sure I’m not forgetting any?”

“Apple Bloom, don’t worry.” the pegasus reassured her, “I’m sure he’ll love them. He always does.”

Never the less, Apple Bloom was still worried that the colt who saved her sister wouldn’t like the apples she was bringing him. She never wanted to disappoint The Doctor, mostly because he was the only friend she had outside of the Cutiemark Crusaders and Derpy. Maybe it was just the way he talked, but the filly felt like he was important some how, not just the her but to all of Equestria. Either way, Apple Bloom was always excited to see the crazy brown colt in the blue box that was bigger on the inside.

As the two reached the TARDIS, a loud bang came from the inside of the box followed by a groan of frustration. Derpy and Apple Bloom ran inside, only to be welcomed by a huge cloud of smoke.

“Doctor? Doctor!” Derpy called out, worried that the colt mite have blown himself up while working on the high tech machines inside. She was answered by the sound of metal falling on a floor and the creaking of hoof steps coming up the stair case.

“Do not go down there,” The Doctor said to his friends, “the spacial reconfigurer is all mixed up with the time racial modulator, and there are all these wires and buttons and ooh! Are those apples?” The time clot was covered is splotches of oil and wearing a pair of goggles, yet his bow tie was remarkably untouched. He opened one of Apple Bloom’s saddle bags and pulled out a bright red apple with his teeth, then took a large bite out of it and smiled. “So good... I love apples, it’s strange how I can like apples and yet hate pairs so much. It really is remarkable.”

Derpy and Apple Bloom couldn’t help but laugh, it had been like this for two months for the three ponies. After their strange friend from another dimension came, life just seemed a bit more... Fun. Even The Doctor had to smile, this place was so different from his Earth. The Earth that always seemed to be under constant attack from strange aliens or evil time lords. Equestria was different, and if he didn’t have loved ones back home The Doctor mite’ve considered staying indefinitely... But he needed to go back. Not only for his sake, but the sake of these ponies. His friends...

***

“HEEEELP!!!” Cherilee screamed as she ran of her life. The school teacher had just left work and was looking forward to a relaxing weekend at home, when all of the sudden a shadowy figure lunged at her and tried to ram her. Luckily, she had dodged the first attack, but now her attacker was chasing her and gaining on the poor school mare fast. She reluctantly looked behind her to see who in Equestria it was, only to be shocked beyond believe. “You... No! Get away!” The pony tripped and looked over at the outline of the Mysterious Mare-Do-Well as the hero closed in on her.

Slowly, the masked pony inched over to Cherilee until the pony was within ramming distance, then the former hero charged. Cherilee closed her eyes and curled up, trying to make herself a difficult target for Mare-Do-Well to hit. It looked like the teacher had lost all hope, but then the swift wings of a pegasus caught her eye. She could tell the pegasus was female, the long, golden hair gave that away, but what she didn’t know was who this brave pony was. Cherilee’s savior reared up, hitting Mare-Do-Well in the head as her wings flapped menacingly. The masked pony had no choice but to flee, the pegasus beating her back with her head hooves.

Cherilee looked up at the pegasus, “Th... Thank you. I... I don’t know what to say...”

“You’ve said enough to me,” the strange pegasus replied, “but I think the mayor would want to hear what happened. If you’ld care to join me.” She held out a hoof and the teacher pony took it. As she got on her own four hooves again, Cherilee turned to her hero and smiled.

“Who are you by the way?” she asked.

The pegasus stayed silent and lead the pony back towards Ponyville, and straight to the office of Mayor Mare.

(Part 1) Heroes of Equestria

Heroes of Equestria

At the crack of dawn, The Doctor woke up to the sound of birds chirping softly outside the doors of the TARDIS. The time colt rubbed his eyes as he stood, his legs shaking from the hard work he had put into his machine late last night. Even with his hooves aching, he had to admit that it was all for nothing. Even with the updated cortex analog and the addition of a new blue whirly thingy, The Doctor knew that the one thing his TARDIS truly needed was power. Normally, it would’ve recharged pretty much automatically, even in a strange dimension like this one, but for some reason the time cortex just wouldn’t absorb anything from Equestria.

“Maybe,” The Doctor pondered, walking into the kitchen and grabbing some bread, “the unicorn’s magic is interfering with the old girl’s mainframe...” He casually popped the bread into a toaster and waited, his stomach growling angrily as the time colt’s mind searched for an answer. “Either way it doesn’t matter. I just need to find something with enough energy to get her running again... Maybe a controlled explosion... Or Pinkie Pie.”

Suddenly, there was a heavy knock at the door, “Doctor!” Derpy’s voice called out, “Doctor, you there? I brought you some muffins! They’re banana-nut... Well, it’s banana-nut...”

The Doctor opened the door and looked at his companion with a raised eyebrow and slight smile, “Got hungry huh?” he asked, his eyes drifting to the lone muffin in the basket.

“Kinda.” the pegasus blushed and walked in, her crossed eyes seemed to pick up on the construction going on everywhere at once, “So... Busy?”

“A little yeah,” He took a bite of the muffin, “mmmm... Did Pinkie make this?”

“No, it’s a family recipe. You’re not... planing on leaving before I say good bye are you?” she asked, turning to face The Doctor.

The time colt looked at the sad look Derpy gave him and gave her a warm smile, “Of course not, I can’t just leave with out saying good bye to you and Apple Bloom. What gave you that idea?” The sound of the toast popping up sent him into the kitchen.

“Well,” Derpy said, following behind her friend, “it’s just that you seem like you’re in a hurry to go, and well... I’m afraid one day I’ll fly over here and just find forest.” She layed on one of the kitchen benches, her eyes filled with concern as The Doctor placed a plate of buttered toast next to her.

The Doctor looked her as straight in the eyes as he could, “Listen, Derpy... You’re my friend. If it weren’t for you, well I’d probably wonder why in Celestia’s name I’m a pony.”

Derpy smiled and snickered a little, holding a hoof over her mouth.

“What’s so funny?” The Doctor cocked his head to the side.

“It just sound’s weird when you say pony sayings,” the pegasus laughed more and dropped her voice down to mimic his, “ ‘Why in Celestia’s name I’m a pony.’ ” The Doctor just shook his head and gnawed on a piece of toast as his mind drifted off to question how he could fix his poor TARDIS.

***

The main road of Ponyville was full of bustling mares, colts, and foals enjoying the sunshine and fresh air. Derpy quickly lead The Doctor to Sugarcube Corner for their weekly visit with Pinkie Pie and the Cakes. Even since the incident with Discord in the Equestria Gardens, the pink pony promised the time colt and mail pegasus a weeks supply of baked goods and sweets until The Doctor had to leave town. Oddly enough, the Cakes seemed to be in more of a rush then usual for a normal Ponyville Saturday, while Pinkie was nowhere in sight.

“Oh, hello dears,” Mrs. Cake greeted the two ponies with her usual smile, “Pinkie’s upstairs wrapping up your weekend deluxes for you.”

“Thanks Mrs. Cakes,” Derpy replied, acting as though the two barkers always rushed around like this, “getting ready for the big day?”

“Oh yes, loads to do, not enough time.” Mr. Cake chimed in, his hooves delicately frosting a huge chocolate cake that seemed to be filled with a sort of strawberry jelly. The Doctor and Derpy rushed upstairs to the party pony’s room, but stopped just outside the door.

“Ready to initiate Operation: Sur-Pies?” Derpy asked her friend. The Doctor nodded, a couple of weeks ago the two of them had made a little plan for today. It took days of careful planing, ever single detail had to be completely perfect or the entire idea would crumble to pieces. Finally, they had settled on a simple, yet deadly method of attack... The two ponies where going to sneak up on Pinkie and yell surprise to make her jump to the ceiling. It was completely fool proof. Slowly, Derpy pushed the door open, she held up her hoof to keep The Doctor at a safe distance, then she threw it down and the two pounced.

“Surpri...” was all that The Doctor and Derpy got out as they charged into the room, where they were greeted by a masked pony wearing a cape and purple hat.

Derpy’s eyes widened as she stared at the costumed pony, “You... You’re... You’re the Mysterious Mare-Do-Well...” the pegasus said with a slight squeak, her eyes lighting up as she stood on her back hooves and bounced a bit.

Then Pinkie Pie pulled off her mask, frowning for the first time that The Doctor had seen. “Um... I can explain.”

***

Pinkie jumped from her bed to a small table in her apartment, her cape flowing with her wild turns and twitches. She explained it all to The Doctor: how her body gave her warning signs throughout the days that told where what kind of danger was going to happen and where (her 'Pinkie Sense’ as she called it), how Rainbow Dash had begun bragging about every little thing she did, and even how she and two other ponies formed a hero called the Mysterious Mare-Do-Well.

“You see,” the pink pony began, talking at her usual quick pace, “Mare-Do-Well protected everypony from bad stuff, like stopping run away busses and saving construction ponies from messed up equipment. So, the mayor decided to give her a day to celebrate all the good stuff me and the other two ponies did to help Ponyville, but no one knows that Mare-Do-Well is actually four ponies except for us, and now you I guess. We all decided to keep it a secret, and now Rainbow Dash helps us out a bit too. In fact, I there are actually six ponies who are Mare-Do-Well!” Pinkie Pie’s eyes widened as she gasped, covering her mouth with her hooves, “I wasn’t supposed to say that! We promised that no one could ever know that Mare-Do-Well is actually Mare-Do-Wells, and I was the one who made us all promise... Wait!” she rushed over to The Doctor and Derpy, the party pony’s usual grin back on her face, “If you two swear never to tell anypony that Mare-Do-Well is five ponies, then it’s not like I told you!”

The Doctor’s head shook with all the information he had to absorb. He really came to accept that Pinkie spoke so fast it could break the sound barrier, but he didn’t have to like it. The time colt looked to Derpy, and his assistant nodded at Pinkie in agreement. “We promise Pinkie.” The Doctor answered.

“Do you Pinkie Promise?” she asked, looking the time colt in the eyes, “Because loose lips sink friendships...”

“I Pinkie Promise.” he replied, sticking out his hoof until he remembered that ponies don’t have fingers.

“Great!” the party pony smiled and bounced happily, “Now I can tell you that the other ponies are Twilight and Applejack and the rest of us.”

“Wait, wait, wait...” Derpy held up her hooves to ask Pinkie to pause, “So you six, the six who can use The Elements of Harmony, are also the ponies who make up the Mysterious Mare-Do-Well?”

“Yep.” Pinkie nodded and smiled.

The grey pegasus couldn’t help but look at her time lord friend, deeply confused about all this. “Doesn’t it seem a little strange that you six have so much... Stuff happening? I mean, two months ago you where captured by Discord and Blackspine, and last week Fluttershy and you fought off a Hydra that was trying to eat Zacora.”

“Zaco-who?” The Doctor asked, never hearing this name before.

“I’ll take you to meet her later, you’ll like her.” Derpy replied, “Still, Pinkie... Isn’t it strange?”

“Strange? Hmmm...” the pink pony put her hoof under her chin and rubbed, pondering, then her face lit up, “Nope.”

Derpy’s hoof hit her forehead in a blur of grey and she shook her head. The pegasus thought it was strange that she had never noticed how weird things became around Pinkie and her friends. “Oh well,” she turned to The Doctor, who was admiring Pinkie’s Mare-Do-Well hat, “let’s get going Doctor. We still need to take Apple Bloom to get those purple flowers from the forest.”

The time colt nodded and grabbed the large boxes of sweets, waving good bye to Pinkie as he walked down the stairs. He walked next to Derpy and smiled, “You’ll get used to seeing that.” Then he walked out the door of Sugarcube Corner, leaving a confused Derpy to ponder what her friend had said for a moment before she ran after him.

***

Mayor Mare paced her office, much like she had done a few months before, her mind running through the facts set out before her. First off, she knew Mare-Do-Well was a hero, in fact it was the mayor herself that made the last Sunday of Spring officially 'Mare-Do-Well Day’. She had seen, with her own eyes, that the masked pony wanted to keep Ponyville safe from natural disasters. Hay, she had even seen the masked hero fight off a rather large scorpion creature near the edge of the Everfree Forest a few months ago.

However, that isn’t the picture Miss Cherilee had drawn last evening. The mayor turned to the pony who brought the frightened school pony in, a pegasus with a light brown coat and a sandy-blonde mane. Her wings looked clipped on by some strange armour that was as black as her hoof tips, and she wore a sandy colored vest with a matching cape and watch. Frankly, to Mayor Mare, this pony looked too upper class to be in her small town, and this wasn’t helped by her Trottingham accent. “Before we go one Miss...” The mayor paused.

“Keeper, just The Keeper.” the pegasus answered, her voice smooth as silk.

“Yes, Miss Keeper,” the older pony closed her eyes, a feeling of deja vu filling her. “I want to thank you for saving Miss Cherilee. Many of the foals of Ponyville would be lost without her gentle hoof to guide them, but as to her accusations...”

“About the masked pony.” The Keeper interrupted.

“Yes, the Mysterious Mare-Do-Well. How do we know this isn’t just some pony’s twisted idea of a prank?” Mayor Mare walked behind her desk and took a sip from her apple juice box.

“That is what I intend to find out Miss Mayor,” the strange pegasus answered, “but I’ll need a bit of assistance.”

“Of course, I can get you the best detectives from Canterlot.” she began to walk towards a shelf filled with scrolls.

“Actually, you have the best detective in all of Equestria right here in Ponyville.”

The Mayor turned to her guest, an eyebrow cocked in confusion, “And who would that be?”

The Keeper smiled plainly, like she was trying to hold back a snickering at the mayor for doing something stupid, then she simply said, “The Doctor.”

(Part 2) The Zebra and the Pegasus

The Zebra and The Pegasus

It took a good amount of time to walk from Sugarcube Corner to Sweet Apple Acres, but The Doctor enjoyed it. Equestria was a good change of pace from his usual adventures in time and space, his fights with hostile alien races, not to mention the ever present threats on his life. However, he knew that he needed to leave as soon as possible, not only to protect his friends and allies on Earth... But to see her again. The only woman as insane as the time lord himself, and the only one just as unpredictable, Melody Pond, or River Song as many knew her. The time colt worried about her, and he was sure that she was just as worried about him. The Doctor shook his head, he couldn’t think about this like that now, not around these ponies who probably knew little of loss. He looked up and ran after Derpy, noticing she had flew ahead.

Sweet Apple Acres was as quiet as ever, at least until the two ponies trotted up to the barn and where greeted with the shouts of ‘Cutie Mark Crusaders Stunt Ponies!’, then where bombarded by the bodies of three fillies. Derpy was hit by Apple Bloom and Sweetie Belle, while The Doctor caught Scootaloo in his fore-hooves.

“Again girls?” Derpy asked, “I thought stunt pony was last week.”

Apple Bloom laughed and jumped off the grey pegasus’ back, “Nope, last week was circus ponies.” The filly turned her head to her flanks, then frowned at the still blank spot.

Sweetie Belle and Scootaloo hit the ground next, then the pegasus filly looked up, “Hey! Where’s my scooter?” she asked, just as the toy fell off the roof and nearly hit The Doctor in the head.

The time colt jumped, standing on his hind legs as he covered his head with his hooves, “I think we should head inside... I’d rather you girls not try for ‘Cutie Mark Crusaders Nurses’.” Apple Bloom lead the group into the kitchen, then reached into the fridge and pulled out a pitcher of apple juice with her mouth. “Anyway,” The Doctor continued and turned to Derpy, “on the way here you where telling me about somepony named Zecora.”

“Oh well,” Derpy took a sip of her freshly poured juice, “I only know a little bit about her. Mostly that she makes herbal remedies for some of the ponies in town. Apple Bloom could tell you more, she was the first one in Ponyville to trust her.”

The farm filly poured the last glass of juice and then began to tell The Doctor about the first time she met Zecora, about Applejack and her friends running through a field of Poison Joke, about when she got the Cutiepox, and even about last Nightmare Night when Princess Luna joined in the festival. As she finished, The Doctor’s eyes brightened as he drained his glass.

“Apple Bloom, you’re brilliant!” the time colt said as he ran out the kitchen door, leaving his companions in the dust.

The three fillies looked at each other in confusion, but Derpy understood when her strange friends meant. Zecora knew a lot of strange magic from where ever she came from, and maybe she had some sort of herb or medicine or something that could help The Doctor fix the TARDIS.

***

“Yes little herb, oh you will do. I need you for my special brew.” a voice shattered the calming quiet of the Everfree Forest as The Doctor tried to get his bearings. He felt he may have been a little bit rash, running into the never ending field of trees before getting directions from Apple Bloom. The time colt felt he was close though, mostly because he had to jump over a flower that looked like the Poison Joke the farm fill had described. He would have to come back and analyze it later, since the idea of a flower that pulled pranks peaked The Doctor’s curiosity. It was about this time that a smell filled the air, the smell of an irresistible vegetable stew. The time colt pointed his hoof in a random direction and closed his eyes, “Einie, Meenie, Miney... That way!” When The Doctor opened his eyes, he was greeted by a zebra in a tattered brown cloak and shining gold necklaces.

“A visitor? Or client still...” Zecora said, “You must be from Ponyville. I greet you with a humble smile, come and stay with me a while.”

“Well, that’s very nice thank you.” he stuck his hoof out to shake, “I’m The Doctor.”

The zebra shook her guest’s hoof and smiled warmly, “A pleasure sir, of this I know. Of my soup we shall share a bowl.” She pushed through a wall of loose vines to open a small door, leading the two to a small clearing with a hut in the middle.

“It’s beautiful here,” The Doctor commented, sitting on a large log near a cauldron of bubbling stew, “I’m guessing you’re a shaman?”

“Intelligent, and very correct. But something like this, I would expect.” Zecora ladled some of the soup into a small brown bowl for her guest, “Because, of course, it’s not every day, that a Time Lord will come your way.”

The Doctor nearly spit out the bit of stew in his mouth, his eyes now on the smiling face of his hostess, “H...How did you?”

“My people, you see, had signs that could tell, whether ponies where good or came from Hell.” Zecora’s rhyme never missed a beat as she chewed on a slice of carrot, “A legend was passed, from my sister to me, of a time when strange ponies came past the sea. One had a cutie mark of sands in a glass, it moves every day as the time of day pass. I noticed this mark when you walked through the trees, which is how I knew you would be friendly to me.”

The Doctor looked to his flank and noticed that his hourglass cutie mark had turned sideways, signaling that it was noon. He had noticed the strange behavior of his cutie mark a few days ago, when it started to spin as he tried to fix the TARDIS. “So, you probably know why I came here too.”

Zecora nodded, but her smile was soon replaced by a frown, “I do not have an herb to help, but information that I must tell.”

“Is it that I’m going to die?” The Doctor asked, “Because I’ve been through that before and I’m still here... obviously.”

“No, nothing to that extreme, but it is important, of that you will see.” The zebra closed her eyes and took a long bamboo stick from behind her log seat, placing one end on the ground she flipped in the air and balanced her head on the other end. She crossed her fore-hooves then began to speak, “Many trials you must see, before returning home for thee,” A deep voice spoke through Zecora’s lips, but didn’t phase The Doctor as he had seen this happen before many times, “One of purple, one of grey, one of blue is all I’ll say. To pass these trials you must, or to return home you shall only lust. But I warn you, son of Galliefray, terror shall come thy way. For the trial saved for last is a trial from the past, for any skill that you may lack will be shown in the trial of black. And for this many will cry, and and this planet may die. You have been warned oh wise Time Lord, now return to your search forlorn.” With that, Zecora opened her eyes and lost her balance, waving her hooves to try and keep from falling flat on her back as she usually did when knocked out of meditation.

The Doctor just stood there in silence, breathing slowly as he tried to brush off what the strange voice that used the zebra told him. “Equestria could be destroyed... Another planet, so many creatures...” The time colt opened his eyes, a look of fear and pain radiated from them as he remembered how his home, Galliefray, had died... And how he had killed it. He shivered in the warm sun, as if the very depths of his soul had been chilled by his thoughts.

“Doctor, what’s Galliefray?” Derpy’s voice broke the silence surrounding the time colt and he turned. Behind hi where his assistant, Apple Bloom, and a new face that he hadn’t seen in his time in Ponyville. The brown pegasus with sandy hair walked closer to the group, a soft, sad smile on her face.

“It’s The Doctor’s home planet,” The Keeper answered, “the planet of the Time Colts and Mares.” She moved her cape, reveling an hourglass cutie mark.

The Doctor looked up at her, she seemed familiar but he knew she couldn’t be a Time Lady. “Who are you?” he asked. The Keeper sat down next to him and began to tell him how she had found the illusive Doctor.

***

The Keeper left Ponyville’s town hall quietly that morning, trying to keep a low profile in this small town seemed to be pretty easy. The mayor even had the helpful hint to run if the time mare ever saw a pink pony with extremely curly hair. Before she began her mission, The Keeper had asked an important pony about any companions The Doctor would have in town. The pony only mentioned two: a mail carrier pegasus with odd googly eyes and a kind disposition, and a filly with no cutie mark and fiery red hair that was tied up in a bow. If she was any other pony, The Keeper would’ve spent hours searching for The Doctor’s companions. However, all the time mare had to do was pull out a small diary where she had written down the details of The Doctor’s stay in Equestria to the last period. All she had to was find the homes of those two ponies and wait.

Derpy Hooves (her informant said that she would change her name to Ditzy after meeting The Doctor) lived in a two story home close to post office of Ponyville. The Keeper couldn’t get much out of her informant about the grey pegasus, other then a love of muffins and her curer as a delivery mare, but from the talk around town Derpy was the first to meet the strange colt that lived in a blue box near the forest. The time mare slowly opened the front door, entering the house as quiet as a mouse. As she trotted into the kitchen, The Keeper couldn’t help but feel a pair of small eyes on her. Inhaling deep, she pulled a small, silver cylinder out of her vest with her teeth and aimed it at the outline of a filly.

Little Dinky had come home from school early, since Miss Cherilee hadn’t come in and the substitute didn’t have enough planned work to keep the room full of foals occupied. The little filly was visibly shaking, but stood her ground, aiming her horn at the intruder. “W...who are you?” Dinky asked, “Where’s my momma?”

The Keeper lowered her weapon, placing it back in her vest as she kneeled at her front legs only and looked the brave pony in the eye. Unlike her mother, Dinky’s eyes never crossed or swirled. “You’re mom’s with a friend sweetie,” the time mare answered, “a better question would be about your father...” She paused as she saw tears well up in the foals eyes, but it was too late to put up that can of worms. With out thinking, The Keeper pulled Dinky close and hugged her, “I’m sorry... I’m very, very sorry...” And for some reason, Dinky Hooves felt like every thing would be ok... Just like she did when her mother held her close.

***

“A few minutes later,” The Keeper finished up , “she told me about how her mom had been hanging out with this new colt most of the time she was at school. Then she asked if she could come with me...” The small grey foal nuzzled Derpy’s leg and the pegasus held her close, apologizing over and over about not being at the house to welcome her home. “After that, we went to Sweet Apple Acres and found these two running towards us.”

The Doctor looked into the strange pegasus’ eyes, his thoughts interrupted by Dinky telling her mother it was ok and that she was a good mom. “You never answered my question,” The Doctor’s eyes narrowed, “who are you? I know you arn’t a Time Lord, they’re all dead except for me. So who are you... Really?”

By this time, Zecora had entered her hut to recover from her possession just moments before. Apple Bloom and Dinky began to play, and Derpy moved closer to the fillies to keep them in the clearing. But the farm filly’s mind was focused on The Doctor and The Keeper, the brown pegasus had told her who she was and it seemed unreal. She couldn’t understand why the time mare told her in the first place, but it scared her to think that...

A rustling in the bush behind her made Apple Bloom jump, then a gloved hoof ripped through the leaves and nearly hit Dinky.The grey unicorn raced to her mother and cried, “She’s here! She’s here!” fear obvious in the foal’s teary eyes. “Miss Keeper! Help!”

With that, the time mare jumped from the log and pulled the cylinder from her vest again. The pegasus’ mouth closed around the trigger mechanism and blasted the bullet from it’s casing, rocketing out of the barrel and flying through the air towards the Mysterious Mare-Do-Well. The masked pony just stood there as the bullet wized over her head by a centimeter, then she glared at her would be assassin.

Just as The Doctor was about to yell for the group to run, he head the sound of something the size of a medium bolder zoom past them. The group watched as a dark purple cape blew in the breeze, followed by a gloved hoof adjusting a light purple hat. There, in the clearing, stood two masked ponies, but only one would be left standing.

(Part 3) The Masked Menace, pt.1

The Masked Menace (Part 1)

Dinky Hooves stared at the two masked ponies, her mouth wide with surprise. The filly smiled and seemed to bounce up and down in a Pinkie Pie-esk manner, “Ohmigosh ohmigosh ohmigosh! Mare-Do-Well! The real Mare-Do-Well... I’ve never seen her so close, and I get to watch her kick the oats out of...”

“Dinky!” Derpy called as she picked her foal up by the scruff of her neck and ran. The Doctor had given the signal to run a few minutes after the second masked pony landed, and Dinky had been lost in her own little world. The grey pegasus knew her little muffin loved the Mysterious Mare-Do-Well, but she also knew that when an evil masked pony is fighting a good masked pony it was customary for all non-masked ponies to run far away... At least that’s what she figured from the comic books that Dinky always had lying around the house.

Ahead of the mother and daughter where Apple Bloom, The Doctor, and the strange brown pegasus who seemed to be reloading her cylinder gun. “You brought a gun?!” The Doctor called out, his hooves tired from trying to keep up with the flying Keeper.

“Of course I brought a gun!” The brown pegasus said, “I always have a gun!”

“But done it always have to be the first thing you go to?!” the time colt asked, “I mean really River!”

“Wait! How did you know it was me?” the brown pegasus asked, sliding the gun back into her vest pocket.

“Oh come on! It was obvious! You know me, you used a gun, and no one else I know can use a time destablizer like you!” The Doctor nodded his head towards the watch on River’s from left hoof.

“Oh I love when you do that sweetie!” the brown pegasus said, smiling almost manically.

“ I know!” the time colt replied, his TARDIS now insight.

***

Back at Zecora’s, the two Mare-Do-Well’s faced each other, still sizing one another up. The second Mare-Do-Well, the one who flew past The Doctor’s head, flapped her wings to try and intimidate her foe; however, the first masked pony just shrugged it off by flipping off her hat and reveling the horn underneath. The pegasus Mare-Do-Well gasped, stepping back just an inch as her opponent pounced. The attacking masked pony stabbed at the other, trying to spear the second Mare-Do-Well with her horn, but the second masked pony was too fast and the horn only cut off her mask.

With her disguise destroyed, Rainbow Dash pulled off her Mare-Do-Well mask and narrowed her eyes at the imposter. “Well? Come on slow poke! Or do you need time to catch your breath?” the rainbow maned pegasus taunted.

Mare-Do-Well just seemed to smile at Dash under her mask, then jumped into the air and flew at the mare. Rainbow nimbly dodged the attack, but her mind raced once she realized that the imposter Mare-Do-Well had wings and a horn. “No way,” Dash shook her head in disbelief, “there’s no way you’re an alicorn!” But this was the least of the blue pegasus’ worries. Soon, she shrugged off the initial shock and bolted after the imposter, leaving her signature rainbow trail behind her.

Rainbow Dash closed in on her target, her hooves just inched away from pounding the fake Mare-Do-Well out of the sky. Then, a noise echoed in the blue pegasus’ ears. It was an odd sound, like something shifting very slowly, and then the imposter seemed to disappear right infront of Dash’s eyes. The pegasus slowed to a stop and looked around quickly, trying to find fake Mare-Do-Well. Once Rainbow Dash turned, however, she only found a purple gloved hoof heading straight towards her nose. She didn’t have enough time to dodge the assault, and the blow broke the blue pegasus’ nose and sent her plummeting to the ground. In a last ditch effort Dash moved her wings slightly, so the wind from her fall would cause her to loop back up, and made a grab for the imposter’s mask. The pegasus’ teeth bit down hard on the silky fabric and she let gravity do the rest, but as soon as she saw the face of her attacker Rainbow Dash wish she hadn’t.

The now unmasked Mare-Do-Well flew after the falling pony, her front hooves pointed at Rainbow Dash’s head. Before Dash could hit the ground, a purple light flashed just below the falling pegasus. A masked pony, this one with only a horn, caught her friend with her magic and swiftly teleported them out of the forest. The imposter landed, a hint on anger in her eyes and she grabbed her mask and put it back on. Fake Mare-Do-Well walked into the Everfree Forest, the strange shifting sound returning as the pony disappeared.

A few moments later, Zecora emerged from her tree house to a chaotic scene. Her yard was covered in large tree branches, one of her logs was broken in half, and it looked like someone had tipped over her stew kettle as they ran away from something. The zebra closed her eyes and shook her head a bit, “From this mess I shall walk away, I can not deal with things like this today!” She turned, her eyes still closed as she slammed her door... Which then fell off the hinges. Zecora just continued to walk to her bed, mumbling to herself.

***

As soon as Apple Bloom entered the TARDIS she noticed something was different. Instead of The Doctor running around the time machine’s consul alone, the brown pegasus who called herself River Song was also pulling levers and turning knobs. And as Derpy and Dinky ran through the door thing got even stranger, as The Doctor kissed River softly on the cheek before pressing a large button that made the TARDIS doors close and started to make the room spin slowly. Both the grey pegasus and the little farm filly knew that this was just what The Doctor’s strange box did when it was moving to a different place (or through space as the time colt put it), Dinky, however, felt like her lunch was going to come back up. The poor grey filly began to wobble on her feet, and was only saved when her mother wrapped her hooves around her. Dinky snuggled against her wall-eyed mother, smiling happily as her tummy began to settle. The foal’s jaw dropped right after though, once she realized what was usually the first thing people and ponies who went into The Doctor’s TARDIS noticed.

“It’s bigger on the inside.” Dinky said.

The Doctor looked to the filly as he pulled the stop switch on the consul, “Yes, well... Better explain. I’m The Doctor. this,” the time colt pointed to the brown pegasus, “is River Song, she’s my wife...” he paused as Derpy and Apple Bloom’s mouths fell open, “What? Well she is!”

Apple Bloom could just barely keep from laughing out loud, while her grey pegasus friend had to bit her lip to keep from giggling. Dinky just looked up at the strange colt as he ignored the two and kept explaining about hoe his box, the TARDIS, was bigger on the inside and could go through time, then he went on to trying to explain how which nearly put the grey filly to sleep.

“Now,” The Doctor continued, looking over at the now stable Derpy, “you never said you where a mom.”

“You never asked.” Derpy replied, “And before you ask, she was at her grandmother’s when I first met you. And what about you? You never said you where married.”

“Well... You never asked.” The Doctor blushed, looking over at River as she just smiled and shook her head to keep from laughing. Suddenly, a bright purple light filled the TARDIS as the sound of a hoof knocking echoed from the door. The time colt ran to answer it, seeing a beaten Rainbow Dash and a masked unicorn entering her ship.

Twilight quickly pulled off her Mare-Do-Well mask and looked toward The Doctor, her eyes tired from the magic used to teleport her friend and her. It was hard enough using the spell on herself, but with another pony it felt like trying to hatch Spike all over again, not to mention the magic needed to find The Doctor’s ship only added to the stress.

“How did... How...” The doctor tried to ask, his head turning to the door, then the two ponies.

“Magic... hard to explain...” Twilight answered, panting slightly, “Pinkie... sensed that Dash was in trouble... Then I saw Mare-Do-Well... What’s going on?”

The Doctor looked to River, the latter shrugged and shook her head. “I only know that it has to do with that masked pony and you,” the brown pegasus said, “anything else is just spoilers.”

“There was... A sound.” Rainbow Dash said, her voice very weak from the fight. “It was like... I don’t know... like something sliding on grass, or something. And then Mare-Do-Well just, disappeared. And...And her face... it was...” The blue pegasus layed down, passing out on the cold metal floor of the TARDIS, her body to tired to keep her awake after the fight.

The time colt looked out the doors of his TARDIS. With the calculations that he and River had made, the ship had phased right behind the Ponyville library. The Doctor closed his eyes, taking a deep breath as he frowned. He knew what was wrong, but he just hoped it wasn’t too late.

***

On the other side of town, a masked pony entered the front door of the Carousel Boutique.

“One moment darling,” Rarity called out from behind a wall of cloth, “I’ll be with you as soon as I finish this dress.” The fashion pony let the fabric fall to the floor, her magic’s aura leaving it after she gasped in shock. “Who... Who are you?”

The fake Mare-Do-Well pulled off her mask and took a step forward. Outside, a blinding light came from the windows of the boutique as the screams of the mashmellow colored unicorn filled the air.

To be continued...

(Part 4) The Masked Menace, pt.2

The Masked Menace, Part 2

The fake Mare-Do-Well took a step toward’s Rarity, letting her mask fall to the floor of the Boutique. The marshmallow colored pony trembled with fear as her attacker drew forward, her own face frozen in shock. “Wha... What are you?! You horrible creature, get away from me!” Rarity cried, using her magic to throw one of her mannequins at the fake hero pony. Mare-Do-Well caught the doll in her hooves and ripped it in half slowly, then turned her attention back to the fashion pony.

Rarity threw everything she could find at the beast of a pony: pins, fabric, and even the cash register at the front desk of her shop. All of it had little effect on this strange attacker, this pony who’s face looked so hideous to the dress maker. As the fake Mare-Do-Well grew closer, Rarity did the only thing she could think of.

“This... Is... The worst... Possible... THIIIIIING!!!!” the marshmallow pony screamed, her high pitched voice echoing through the air. Suddenly, the large window on the left end of the boutique shattered as a masked pony jumped through. The fake Mare-Do-Well turned her head, it’s gaze meeting with another masked pony. This pony, however, didn’t seem to have time to put on her entire costume, as her mane of cotton candy colored hair bulged out from the hem of her mask.

“Rarity! Are you ok?” Pinkie Pie called out, “I heard screaming and then my hoof started tapping the ground while my teeth chattered, and I figured out a while ago that a combo like that meant one of my friends was in trouble. So, I cam zooming to the rescue!” The party pony looked toward the front of the store and finally saw the fake Mare-Do-Well. “Woah! You look like you could use a facial. Either that, or you’re some evil thingy...” Pinkie ducked as the false hero threw half of a mannequin at her head, “I’m gonna go with evil thingy.”

The fake Mare-Do-Well reached out and grabbed a metal bar from the torn up doll, then charged at Pinkie Pie. She cut through the air with the pole, aiming for the pink pony’s head. Luckily for Pinkie her Pinkie Sense was working in full swing, and she dodged before the bar even came close to her. The party pony then tried tripping the fake Mare-Do-Well, but it backfired once Pinkie’s hoof hit the false hero’s back hooves.

“Ow! It’s like you’re legs are made of rock!” the party pony took off her mask and stuck her right front hoof into her mouth, sucking on it to try and stop the pain. “Lucky for me, I brought my loyal sidekick! Choppin’! The Green Wonder!” Pinkie then ran outside and tossed a familiar looking alligator at her foe. Gummy, disguised by a small black domino mask and black cape, quickly opened his mouth and started ‘biting’ the fake Mare-Do-Well. The masked pony shook her head, trying hard to dislodge the little green lizard, but this only made Gummy bite down harder. The minor annoyance was all Pinkie Pie needed, she ran to Rarity and pulled her out of the boutique. The marshmallow pony slid out, stand frozen with a slightly dumbfounded look on her face.

Moments later, a now masked Pinkie Pie ran out of the shop with her costumed croc on her back. Rarity quickly followed, not wanting to know what the party pony had done to her attacker, and definitely not wanting to stay just incase the fake Mare-Do-Well returned. “Pinkie,” the fashion pony asked her friend, “where are we going?”

“Twilight Sparkle’s house civilian!” Pinkie answered, wanting to stay in character with the chance of the two being seen, “And please, refer to me as The Mysterious Mare-Do-Well! Thought, this Pinkie you speak of sounds like an amazingly super awesome pony!”

Rarity rolled her eyes, but continued to follow. In her mind, she kept seeing the disturbing face of the fake Mare-Do-Well. To her, a pony who’s soul craved beauty, that...That thing was a monster. A monster that could rip heavy mannequins and cash registers in two! As they neared the library, Rarity began wishing that they where fighting Nightmare Moon again. At least then, the fashion pony would know what they’re up against.

***

Under a large pile of broken stone and wood, made from a hole in the ceiling of the Carousel Boutique, Mare-Do-Well kicked her way out. She couldn’t figure out how she lost the battle with Pinkamina Diane Pie, she presumed it was when the pink pony ducked behind a support beam for the shop to keep from being hit with a metal pole, but for now it didn’t matter. According to her master, all six of the Element users and The Doctor would be at the library by this time. Slowly, the fake Mare-Do-Well shook the rubble off of her outfit and unfurled her wings. Then, she began to make her way to the home of Twilight Sparkle.

***

“Will she be ok?” Dinky asked The Doctor as he covered up Rainbow Dash. The TARDIS didn’t seem like a welcoming location for the blue pegasus to wake up in, so the group had moved into Twilight’s home. The Doctor tucked his Sonic Screwdriver into the band of his bow-tie and nodded to the grey filly.

“She’ll be fine, just a little wobbly when she wakes up,” the brown earth pony replied, “I’m more worried about you. You seemed a bit scared when the fake Mare-Do-Well found us Dinky.”

The foal looked away, blushing with embarrassment, “Well... Miss River told me about her, and... It’s scary thinking that Mare-Do-Well would hurt anypony. She’s the town’s hero...”

The Doctor nodded and kneeled his front hooves down to get eye level with Dinky, “I know, but it’ll be ok right? I mean, your mom’s here. Twilight’s here. And I promise nothing bad will happen to you.”

The grey foal looked up at this strange colt, the odd smile on his face actually made little Dinky feel a little better. “Do you like my mommy Mr. Doctor?” the filly asked.

“What? No,no, no... No. I’m spoken for, and I wouldn’t have any other woma... Um, mare in the universe.” The Doctor eyed the doorway and smiled, “And you can tell that to River when you get out into the hall!” he yelled the last part as loud as he could. Next to the door way, River Song blushed and shook her head.

“I hate when you do that.” the brown pegasus called out, looking into the room as her husband smiled back at her.

“I know, that’s why I do it.” the time colt walked out of the room and River gave him a small peck on the cheek, causing The Doctor to stumble a bit.

“I’ll just...um... yes, well...” he continued down stairs, trying to figure out how she always got the upper hand by doing that. Dinky followed, smiling at River as she passed. “So, Dinky,” The Doctor looked to his new friend, “do you know why your mom didn’t tell me about you?”

“Yep,” replied the little filly, “she said something about you being a secret, and that if you didn’t know about me I’d be safer.”

The Doctor stopped for a moment and mulled what he had just heard, then nodded. “That makes sense.”

In the main room of the small library, Applejack had already arrived. She had gotten Twilight’s note from Owlowiscious just seconds after finishing her chores for the day, and hurried over to the purple unicorn’s home after quickly grabbing her Mare-Do-Well costume. “Now, you’re sure you want ta stay, Apple Bloom?” the farm pony asked her little sister, “It aint goin to be a walk in the park sugar cube. If this imposter was able to knock out Rainbow Dash, we’re not dealing with a run of the mill pony.”

“I know that AJ,” the yellow filly said, “but I just can’t let ya’ll fight off this thing while I just sit in the background! Derpy and The Doctor are depending on me, and you keep forgetting I helped beat Discord and Blackspine.”

“Helped beat?!” Applejack shook her head, “You got mesmerized by that low down snake in the grass Blackspine! I don’t want you ta go through that again Apple Bloom! Now either you go home, or you leave this up to the adults.”

Tears began to form in little Apple Bloom’s eyes as she turned from her sister. The farm filly then ran out the door to the library just as Fluttershy entered.

“Is Apple Bloom ok?” the shy pegasus asked, her voice so quiet that only Applejack could hear her, “She seemed upset... Should I...”

“No Fluttershy... I’ll go.” AJ began to run out the door, “I shouldn’t have lost my temper... Dang it!”

The Doctor suddenly popped up behind Fluttershy, having watched the whole scene from the stairwell with Dinky, “Well that was fun!” he called out.

Needless to say, the yellow pegasus jumped onto the ceiling. “Oh... I’m sorry Doctor. You startled me.”

“Sorry Fluttershy, but I needed to get everyones attention.” The Doctor walked to the middle of the room, everypony as well as Spike looked to him. “Good... Now, I think I know what we’re dealing with. If I’m right, and I try to be right as much as I can, the fake Mare-Do-Well will be coming here in any minute. For my plan to work, I’m going to need Twilight to work up a net while Derpy goes home.”

“Wait, what?!” the cross eyed pegasus stepped forward, a look of conviction on her face, “I can’t just leave Doctor, what if you need me?”

“I don’t Derpy.” The Doctor said with little emotion, “I really don’t... Now go home.” The time colt looked into his friend’s eyes as well as he could, no motions radiated from them at all. The grey pegasus opened her mouth to say something, but then closed it. Tear began to well up in her eyes as she stepped back, struggling to try and keep a small amount of her composure.

“Dinky,” she said, “it...It’s time to go home.”

The little grey filly looked to her mother, a pained look on her face as well... Then she turned to The Doctor. “You’re a mean colt Mr.Doctor!” Dinky called out, ignoring her mothers scolding calls to stop, “My mommy’s been your friend since you came to Ponyville, she’s been nothing but nice and you treated her like Diamond Tiara treats...well everypony! And you said all those nice things to me, but you’re nothing but a...A jerk!” The Doctor looked away from the little foal, and Dinky had finished speaking her mind. She looked at her mother, who still had tears in her eyes, and then followed her as the two grey ponies left.

“I need that net Twilight...” The Doctor said, turning away from the remaining ponies and dragon in the room. The Doctor headed upstairs as the sound of hooves filled the quiet house, sounds loud enough to help The Doctor cover up the sounds of a couple of tears hitting the floor.

***

Pinkie Pie knocked loud on the door to the library as Rarity shouted at the top of her lungs.

“Twilight! Darling! Let us in!” the fashion pony called out, looking over her shoulder at the form of the fake Mare-Do-Well closing in on them. Suddenly, the door to the library opened and the two ponies stumbled in. “She’s right behind us!”

“Who?” Fluttershy asked as she hid behind a table. Twilight had just finished making the net The Doctor wanted, her mane a bit of a mess but nothing big. She could fix it after dealing with the insane alicorn that was trying to kill her and her friends.

Just as Pinkie had moved away from the door, it burst open again to revile the fake Mare-Do-Well, her masked ripped open to show a small portion of her face. Fluttershy couldn’t believe her eyes, she had never seen a pony like that before. It looked like... Like a monster!

Quickly, Twilight threw the net over the false hero. However, the masked alicorn slashed through the rope with her horn, then made a blind charge for Twilight. The purple unicorn teleported out of the way, just in time for The Doctor to jump out of the kitchen. His plan was working perfectly, and he aimed his Screwdriver at the charging Mare-Do-Well. Quickly flipping it on, the fake hero came to a complete stop and fell to the ground with a loud clang.

“Exactly as planned!” The Doctor called out.

“Exactly as... You said the net would stop her!” Twilight called, her teleport spell moved her on top of the table Fluttershy was hiding behind.

“I said I needed the net, never said it would stop her.” He smiled as Celestia’s number one pupil glared at him, “Now, let’s see who the Mysterious Mare-Do-Well really is gang.” The Doctor paused and waited for the other ponies to laugh, “See... It’s funny because it’s a Scooby-Doo reference.”

Fluttershy poked her head out from behind the table, “What’s a Scooby-Doo?”

“Right.. forgot I’m not... Anyway, let’s see who you are...” The Doctor bit the end of the masked pony’s disguise and ripped it off, making Twilight and Fluttershy gasp. Under the dark purple mask was a pony with bark green metal skin, instead of eyes it had a sideways hourglass shape, and instead of a mouth there where markings like a human would find on a microchip.

“Doctor...” Twilight sadi, her voice shakey, “What is that?”

The Doctor turned to Twilight, a smile on his lips that slightly unnerved the purple unicorn. “This... Is a TARDIS.”

Suddenly, the TARDIS Mare-Do-Well’s entire body opened, and a greenish brown colored mare with long dark brown hair stepped into view. She wore an all red outfit, including a cape, and as she turned an hourglass cutie mark began to come into view. Her eyes narrowed as she saw The Doctor, and she smiled menacingly. From her front pocket she pulled a metal tube, much like River’s gun, but with a small red ball at the end. “Hello, Doctor.” she said, her voice sweet yet powerful at the same time.

“Hello... Rani.” The Doctor replied.

Author’s Note: It’s time for Doctor Who Trivia! This is just a little thing to help non-Doctor Who fans understand what just happened. Now, The Doctor says he’s the last of the Time Lords (an alien race that can travel time in TARDIS’) but he’s kind of lying... He does that.

There are actually four more Time Lords: The Monk, The Master, The War Chief and The Rani. I’m going to focus on The Rani (pronounced Ron-nee). The Rani is a female Time Lord, or Time Lady, who also has a TARDIS. Her TARDIS has a working Camelion Circuit, which allows her to change how it looks on the outside. The Doctor’s broke, which is why it’s stuck looking like a police box (a sort of blue phone booth). The Rani also is an evil genius, who uses her time travel abilities to try and get test subjects for her experiments. She views everything as a test subject, which includes humans and (most likely) ponies. She and The Doctor have faced off a few times, with The Doctor coming out on top. Well... Hopefully that cleared up a bit of questions. As for The Monk, The War Chief, and The Master... I’d go to Wikipedia to look them up because I only know about the Master, and well... Spoilers.

See you next time as The Doctor and his pony allies face off against The Rani in The Purple Fear.

(Part 5) The Purple Fear

The Purple Fear

The Doctor was actually very surprised that it was The Rani who was facing him, a strange weapon between her pony teeth that was aimed straight at him. He hadn’t seen the time lady in years, but here she was standing right in front of him in a fully pony body.

“I know what you’re thinking dear Doctor,” The Rani said, “‘why is The Rani a pony?’ Well, I’ll tell you how I happened upon this world, this... Equestria...”

“Fell through a hole in time.” The Doctor interrupted, faking a yawn just to spite his old foe.

“H...How did you know?”

“Well... I got here through a hole in time. It’s pretty much an easy answer, like two plus two equals four. My only question is why The Rani, the second most brilliant Time Lord in existence, needs a TARDIS shaped like an alicorn.” The Doctor walked over to the now closed Mare-Do-TARDIS, his Sonic Screwdriver analyzing the machine and coming back with results that made the time colt whistle, “One that can move, fly, and even travel through time still! How did you manage the repairs on your TARDIS?”

The Rani chuckled at her old friend, “Come now Doctor, I was the greatest mind in the history of Galliefray. You really think I can’t repair my own TARDIS? Even a simpleton can fix a TARDIS’ time cortex.”

“Well you don’t have to rub it in.” The Doctor interjected.

“As for why I need a working Mare-Do-Well TARDIS... I’ll let my new invention answer that.” The time mare aimed her strange weapon at Twilight and fired, sending what looked like a wave of Twilight’s own magic straight at her. Before the unicorn had time to move out of the way, the purple wave hit her and knocked her back. Suddenly, Twilight Sparkle’s eyes pupils grew small, and her mane seemed to shift to where some hairs were sticking out.

“T...Twilight?” Fluttershy stood and edged a bit closer to her friend, “Are you ok?” The unicorn then turned to her timid friend, a blood chilling smile breaking across her face.

“Oh I’m just FINE Fluttershy.” Twilight answered, talking through her insane grin, “But you must have some sort of problem with your eyes, right? RIGHT?! I mean... Let me help you with that, my friend!” The purple unicorn’s horn started to glow, and she fired a beam at Fluttershy’s face. The yellow pegasus quickly avoided the attack, but couldn’t avoid the second bean of magic. Fluttershy turned to face where she thought the door was and ran, only to hit a wall. The Doctor stood over her to see that the animal loving pegasus now had her eye lids fused together.

“What have you done?!” The Doctor turned and dashed at The Rani, hoping to hit her and knock the device from her mouth, Instead, he hit the door of the library as Applejack walked back in.

“I’m sorry ya’ll, I couldn’t find Apple...” AJ was then cut off as The Rani fired another wave of purple energy, this time at the farm pony. Applejack’s mane became messy as well, and she started to grow bags under her eyes.

The honest pony yawned, then her eyes opened wide. “Oh no! The harvest! I have to get the crop down, now!” Quickly, Applejack ran in the direction of Sweet Apple Acres just as The Doctor stood back up.

“Are we going to be civil now, Herr Doctor?” The time mare now had her machine aimed at the brown pony again, “Good... Then I’ll explain my little friend here. This,” The Rani gestured to the cylinder with her hoof, “is a little thing I’ve named The Purple Fear. You see Doctor, I’ve been here quite a long time, years in fact, and I’ve noticed one constant variable in every single pony throughout all of Equestria. They all have a moment where they break down in complete, and utter fear. For Twilight Sparkle, it was the fear of disappointing her beloved Princess Celestia so much, that she would be sent back to...”

“MAGIC KINDERGARDEN!” Twilight yelled out, almost on cue.

“... Yes, well... And dear sweet Applejack feared that her family would lose their home if she didn’t harvest all the apple in the orchard a couple of seasons ago. The Purple Fear uses a psycho-hypnotic wave to alter a pony’s mind to take them back to that point of pure fear. Now, in theory it should work on humans as well, but why try to return to our own universe alone when I could have an army?!” The Rani chuckled manically, then turned her gaze to Pinkie Pie and Rarity who where hiding in a corner of the library.

“As for the Mare-Do-Well disguise, for now it’s to blend in and gain trust.” the time mare continued, “With all of Ponyville at my feet, it will be simple to move on to Canterlot, Trottingham, Stallionguard, The Dragon Empire, The Griffon Democracy, and then... Earth!”

“That’s all I needed to know,” River Song said, she had stayed on the staircase since the net was thrown. Now, she held her cylinder gun between her teeth and aimed at The Rani, “now get away from my husband.” The light brown pegasus fired, but her bullet was blocked by the body of the Mare-Do-Well TARDIS.

“You think I didn’t account for you, little miss Pond?” The Rani laughed as her TARDIS stood triumphantly. “You don’t think I would program my TARDIS to save me from any threat that may come my way? You’re a fool Song, just like your husband.” Her eyes turned back to where the Doctor was, but he was gone. With a quick look around, The Rani could see that Twilight and her friends had disappeared, and only she and River remained in the room.

“All part of the plan.” River jumping into the TARDIS as it began to dematerialize.

***

“Thank Celestia for Pinkie Pie!” Rarity called out, hugging the party pony, “I never knew you could move so fast darling.”

“Well, I did beat Rainbow Dash in a race once.” Pinkie responded.

“Well it was brilliant Pinkie,” The Doctor walked back into the control room. River had been piloting the TARDIS as he placed Twilight in the medical bay, strapping her to a bed to keep her from 'helping’ anypony. Rainbow Dash still hadn’t regained consciousness, but they group thankfully had enough time to shift upstairs to grab the fastest flyer in Equestria.

“What now Doctor?” Fluttershy asked, her eye lid where still fused together, but she opted out to have Rarity push her around in a wheel chair.

“We need to find Applejack before she causes too much trouble,” The time colt began, “then we need to find Apple Bloom. After that... I... I don’t know...” The Doctor sat on the cold metal floor of his TARDIS, a look of deep concern on his face. “There has to be some way to stop The Rani, but we’d have to get close enough to get The Purple Fear away from her. And the only way to do that, would be to keep the Mare-Do-Well TARDIS preoccupied with an equal threat to The Rani or her plans.”

As the time colt sat there, a hoof on his chin as he pondered, River looked over at Pinkie Pie. “Pinkie,” the brown pegasus began to ask, “do you still have your mask to go with that costume?”

“I sure do, and the hat! And my sidekick, Choppin’! The Green Wonder!” The pink pony reached under her cape to pull out the still costumed Gummy. “Why do you ask?”

“I have an idea... But I’ll need your help.” River then turned to her husband, “Doctor... I think I’ve found our threat.”

The Doctor looked up at Pinkie Pie and smiled wide, “Bloody brilliant...”

***

Dinky paced her room slowly, grumbling and crying at the same time. “That Mr. Doctor wasn’t nice at all... Momma said he was the nicest colt she knew, that he didn’t say a single mean thing to her... But then he....” Dinky focused her magic on her stuffed Mare-Do-Well toy and threw it at her book shelf hard, causing some of the books to fall to the floor.

Derpy sighed as she watched her daughter, feeling the same anger she did. How could The Doctor treat me like that? How could he be so cruel, she thought. Was I just some dumb pony to him? Was everything he said a lie? It didn't matter now, after all he had told me..Then it hit her like a ton of bricks, the cross eyed pegasus smiled brightly and said the words she had nearly forgotten. “The Doctor lies...”

Quickly, the grey pegasus bust into her daughter’s room and hugged her tight, kissing her forehead softly. “Dinky, lock the doors and don’t let anypony in! Not even me, ok? Only let me in if I’m with The Doctor.”

“What?” the little filly replied, a look of confusion on her face, “But he’s a meanie butt!”

“Trust me muffin,” Derpy kissed her daughter on the cheek, “he’s not a meanie butt.” She then dashed down the stairs, slammed the door behind her. If she could find the TARDIS, she had a chance!

To be concluded...

(Part 6) Time of the Hourglass

Time of the Hourglass

The Mayor of Ponyville walked onto the stage, her knees visibly trembling as she got behind the podium. It had been almost a week since she had hired The Keeper to find out what had happened to her town’s former hero, but Mayor Mare hadn’t heard a word from the strange pegasus after she had left town hall. Now, she had received a letter only moments ago from an unknown pony. The grey maned mare could had memorized it down to the last period...

To the Mayor of Ponyville,

I wish to address the colts, foals, and mares under my protection at exactly 3:33 PM today. You have three hours to call as many of the citizens of Ponyville to town hall, that is all.
Sighed,
M.M.D.W.

It hadn’t taken long for Mayor Mare to figure out who the author of the letter was, after all who else would have so many initials in their name? She had tried various times to contact her detective, and even went so far as to try and find the blue box that The Doctor lived in but to no avail. The Mayor had nearly asked her assistant to bring in a couple of mugs of cider, but she knew it would only make the ponies fear even more to see their mayor tipsy on stage. She looked out to the crowd and could see so many familiar faces: from Big Macintosh, to Miss Cherilee. In fact, Cherilee’s presence is what scared the old mayor the most. If word got out that an important, and upstanding member of Ponyville was attacked by what many believed to be the town’s greatest hero... Well, who knows what would happen!

Mayor Mare looked to the side of the stage, then gasped as she spotted Choppin’, the Green Wonder, staring right back at her. If Mare-Do-Well’s animal sidekick was here, that means the masked pony was sure to come soon.

“Attention... um... Hello?” Mayor Mare spoke into the microphone, causing the group of ponies to stop chatting among themselves and focus on her. “It’s time to tell you all why we’re here, but... It’s a bit difficult for me to explain. A few nights ago, Miss Cherilee... Could you come up here dear?” The mayor paused to let the school teacher trot up to the stage, “Miss Cherilee was attacked by, what she describes as, The Mysterious Mare-Do-Well.”

The crowd gasped in shock, many of the foals went wide eyed, but Big Mac didn’t move from his spot. “Miss Mayor,” the red pony said, “Are ya’ll sure it was Mare-Do-Well? That don’t sound like her to me, and everypony’s thinkin’ the same thing. Even you, Miss Cherilee.”

“That’s true Big Macintosh,” The mayor continued, “but we cannot rule out that it was her... Now, this meeting was actually organized by Mare-Do-Well herself. I’m sure she’ll have an answer for everything.”

“Oh believe me, I do.” said a deep, yet obviously female voice from the back of the crowd. Everypony turned, and their manes all stood up on their ends as the Mysterious Mare-Do-Well made her way to the stage. She stood next to Mayor Mare, who seemed to be guarding a shaking Cherilee. “First off, I would like to apologize to any and all ponies whom may have been hurt within the past week.” the hero began, then turned to the teacher pony, “Especially to you Miss Cherilee. You see, there’s an imposter pony running around our fair Ponyville, dressed as me. My plan today, is to prove to you all that I am the real Mare-Do-Well.”

“How’re you going to do that?!” a voice in the crowd called. Once more, everypony turned, but this time they saw The Doctor and River Song step into view. “If you’re the real Mare-Do-Well, why don’t you fly? Or use your magic?”

The masked mare on stage didn’t move, instead she just leaned forward towards the microphone. “Because, I cannot perform magic. I cannot fly... The ones who could do that where my allies in the battle against the disharmonious forces that plague Ponyville from time to time, but please mares and gentlecolts believe me. I AM The Mysterious Mare-Do-Well!”

“A truly pathetic turn of events Doctor!” yet another voice called from behind the crowd, but this time nopony tuned. “Hello? Didn’t you all hear me?!”

“Yes,” Big Mac called out, “but we’re sick of turnin’, so please just walk to the stage. Thank you kindly.”

“Fine! Useless pony ingrates...” The Rani mumbled, as she and the TARDIS-Do-Well approached the stage. “Now as I was saying, this Mare-Do-Well is the fraud! I am the master of the true Mare-Do-Well, and you shall all see her power and fury! Mare-Do-Well, I command you to unmask this lair... Then, unleash the power of Purple Fear onto all of Ponyville!” Slowly, the false hero pulled the other masked pony close, its horn at the bottom of the first Mare-Do-Well’s mask. “Now, see as I unmask this fraud... Who I’m sure is none other then Pinkamena Diane Pie!”

The horn of the TARDIS-Do-Well sliced off it’s foe’s mask, but instead of a poofy cotton candy mane underneath it... There was a shinning, silky purple mane. Rarity smiled slightly, the sort of smile everyone gets when they’re scared out of their minds. “He he... Hello darling, who does your mane?”

The Rani just stood there, her mouth nearly dropping to the stage floor. Suddenly, there was a whistle of fabric on the wind, and a figure landed on stage. She had a purple and dark blue costume like the others, but with no hat her horn showed. Her wings flapped under the billowing cape she wore, and the Mysterious Mare-Do-Well charged at The Rani’s TARDIS. Cutting the mask of the machine off, the crowd of ponies gasped once more as their eyes took in the green metal, and even The Doctor had to admit his plan almost failed.

***

“Alright!” Pinkie Pie said, saluting The Doctor, “I’ve got it, completely and undeniably! Every bit of info, right here.” The party pony pressed her pink hoof against her poofy perm, but paused quickly and looked at her friend once more, “So... just incase River missed it, can we go over it again?”

The Doctor rubbed one of his front hooves on his forehead, but smiled as he looked back at Pinkie. He knew it wasn’t her fault she had a hard time remembering the plan, in fact everyone did. So, the time colt took a deep breath and stated it again. “When the Mayor announces the Mare-Do-Well was the pony who asked for the assembly, you come in from the back of the crowd and get on stage. Then, River and I ask you to do magic and fly, and you say...”

“I can’t?” Pinkie asked, then saw the brown colt nod, “But I’m absolutely the real Mare-Do-Well.”

“Good, now...” The Doctor continued, “Spike has ‘accidently’ dropped a letter near Fluttershy’s home near the Everfree Forest, and loudly announces to nopony that he hopes he can find the ‘message for The Doctor’.” The time colt used his front hooves to gesture the air quotes to his allies, “After which, The Rani’s TARDIS will be bound to pick up any mention of my name, and steal the letter. The message will be a copy of the letter I sent to Mayor Mare just one hour ago. The Rani will order her TARDIS to unmask you, the machine will perceive you as a big threat to her mission, and while you and it are fighting River and I retrieve The Purple Fear. Any questions?”

“No sweetie.” River answered, loading another bullet into her cylinder gun and winking at The Doctor.

“Nopey-Dopey!” Pinkie replied.

“N...No.” Fluttershy said, happy that her eyes kept her from such a dangerous mission.

“MAGIC KINDERGARDEN!” shouted Twilight.

“Good! Then let’s go...” The Doctor began to make for the exit, but was soon stopped by Rarity. The fashion pony looked at her pink friend, then back to The Doctor.

“I want to help...” She said, her voice just a bit louder then Fluttershy’s, “I want to be the bait instead of Pinkie.”

“Ok... Why?” The time colt asked, his eyebrow cocked in confusion.

“Every time that Twilight, or Pinkie Pie, or... Or any of my friends put on the costume I designed they put their lives at risk.” Rarity looked away, wanting to hide the tears in her eyes, “My Element is generosity, yet... I havn’t taken the burden of defending Ponyville off my friend’s hooves at all.”

“What about the...”

“The Elements don’t count Doctor, you know as well as I that they need all of us to work their magic.” Rarity walked over to her pink friend, and took the purple hat from her head, “It’s as if... As if...” The tears welled up in the marshmallow pony’s eyes, but then she felt a soft hoof on her back. She turned and saw Fluttershy, her eye lids still fused together, rubbing the white mare’s back.

“Rarity,” the yellow pegasus began, “you made Mare-Do-Well possible... You made our costumes. If... If it wasn’t for you, none of us could’ve taught Rainbow Dash her lesson. None of us could help the town in secret...”

Rarity smiled at her pink maned friend, then hugged her tight. However, Fluttershy didn’t see the dress designer take the rest of Pinkie Pie’s costume... Nothing was going to stop Rarity from doing exactly what she felt she needed to do.

***

The TARDIS-Do-Well dropped Rarity, it’s horn breaking off as the marshmallow unicorn cut it with her magic. The mechanical monster then charged at the new Mare-Do-Well, making a sound that was like a growl put through a voice filter. Quickly, Mare-Do-Well flew into the air, but her wings where no match for the pony-shaped TARDIS. Meanwhile, on the ground, The Rani dove for the Purple Fear hidden in the broken horn, just at Rarity tried to do the same. However, the time mare beat her to it, and was now staring into the eyes of The Doctor.

“Finally... It comes down to this,” The Rani began, “an absolute victory over you, Doctor. Just think of it, an army of my experimental creatures invading our dimension’s Earth. Each one doing my bidding, without question or thoughts. Just my voice, ringing in their heads to find more of test subjects... Maybe I’ll start with the Ponds.” The Rani shot and evil glance to River, smiling as she saw the glare the pegasus gave her. “Now,” the time mare pointed the horn at the two time ponies, holding it tight with her teeth, “say good-bye.”

“DOCTOOOOOR!!!!” came the cry of Derpy Hooves as she flew at the stage, her normally crossed eyes now focused on one target: the evil looking mare on stage. The grey pegasus tilted her head down, and aimed her body at The Rani. As soon as the time mare saw it coming, it was too late. The mail carrier pony tackled the dark green mare down, causing the strange device in The Rani’s teeth to fall to the dirt below. There, The Doctor quickly smashed The Purple Fear with his front hooves, stomping it over and over until it became dust. Soon, another whistling sound echoed through the town square, as the fake Mare-Do-Well fell to the ground and shattered. The Mysterious Mare-Do-Well floated down after, but before the ponies of Ponyville could cheer for her, she was gone.

Epilogue

Epilogue

Pinkie Pie ran to the TARDIS as quickly as she could, her hooves barely making a sound as she left the town square through a dark alleyway. Once back at the big blue box, the party pony quickly pushed the doors open and jumped inside. Pinkie then pulled off her mask, revealing the fake horn River had strapped on her head. Then she literally jumped out of her costume, which was modified to have a set of working mechanical wings. Rarity had been trying to find a way to get an idea like that to work without magic, but The Doctor’s weird machines seemed to be a type of magic all by themselves.

“Fluttershy?” Pinkie called out, “Are you there?” Slowly, a cloaked figure slinked out of the medical ward and walked up to the pink pony. Zecora smiled, and lead her friend to the yellow pegasus’ bed, where Fluttershy was happily reading an eye chart.

“All is well, friendly baking pony.” the zebra said to Pinkie, “A salve of berries was needed, and that only. As for Twilight, I’m happy to say, she has made a full recovery today.” On the other side of the room, Twilight Sparkle was already telling Spike to write a letter to Princess Celestia on today’s events. After a while, River Song and The Doctor rejoined the small group, and traveling right behind them was Derpy and Rarity. The two mares where chatting about how exciting it was to see action like that... But then laughed as if they had told a good joke.

The time colt turned to face his grey pegasus friend, an apologetic frown on his face. “Derpy... I’m sorry I...”

The mare placed one of her grey hooves on her friends lips, and smiled happily. “I understand... You didn’t want me or Dinky hurt.” Derpy smiled softly, and kissed him on the cheek. The Doctor blushed a deep red, then quickly turned to his wife and smiled awkwardly.

“Ri... River, you know that I... And I didn’t... Just let me...” Once again, the Doctor was silenced by a kiss, this time one from his beloved River Song. She smiled at him, the time lord who saved her once, then watched as he passed out on the floor.

Derpy turned to River, as Zecora and Pinkie helped The Doctor to a bed, and asked, “Does that happen often?”

“More then you know.” Professor Song winked at the grey pegasus, and the two of them started to laugh.

***

A few hours later... “So...” The Doctor began, a bandage on the side of his head, “You found her... And knocked her out. Then you pulled her here, with Big Macintosh’s help?”

“Yup.” Apple Bloom smiled happily, her sister standing next to her.

“She thought it was the best thing to do at the moment...” Applejack replied, then took off her Stetson to show the time colt the large bump the farm filly had given her. All The Doctor and his friends could do was laugh, and even Big Mac joined in. However, as the group was clutching their sides, The Doctor took River Song by the hoof and pulled her out of the TARDIS and into the forest.

“I know what you’re going to say...” River began, her eyes starting to fill with tears, “And you’re right.”

“I’m sorry River,” the time colt said, his eyes looking deep into his wife’s, “but you know what’ll happen if you and I are here too long.”

“Yes... A time paradox. The end of time... Not here, but in our dimension... Just like old times, huh sweetie?”

“Yeah...” The Doctor then stood on his hind legs and walked over to River, hugging her tight as she cried, “I’ll come back as soon as I can... I promise.”

“I know...” the chestnut brown pegasus smiled sadly, then stepped away from her beloved and adjusted the watch on her right, front hoof. “Allons-y.” She said softly as she disappeared thought time.

The Doctor stood, staring at the spot for the longest time. Then, he started to walk back to the TARDIS... The sounds of his hooves covering his falling tears.

***

13 years later... River Song rematerialized in a large glass room, her hooves a bit shaky from this dimension’s version of quick time travel. The time mare quickly left the room, entering a large, military-like base with only a few ponies inside. A white unicorn mare with purple and white hair walked up to the pegasus, the unicorn’s cutie mark was a small silver bell with a long blue handle.

“Are you ok River? Do you need a drink?” Sweetie Bell asked.

“No thank you Sweetie, I’m fine.” she answered back, she took a step but was greeted by another pony. This one was an orange pegasus with a ruffled purple mane, her cutie mark was a rainbow colored cloud with a purple lightning bolt coming from it.

“How did it work? Did I get all the bugs out?” Scootaloo asked, her eyes wide as she looked at the watch on River’s hoof.

“Not quiet Scoot... Almost, but the landing was wobbly.” River Song then turned to the third member of the trio, a pale yellow earth pony with a long red mane. On the top of her head was a Stetson, and on her flank was an apple surrounded by the white flower petals. “You where right AB, you did knock her out.”

“Told ya!” Apple Bloom replied, adjusting her sister’s hat. “So everything’s fine now, right?”

“Absolutely, time line’s all fixed. You should tell your boss...” the brown pegasus told the trio, who still called themselves The Cutie Mark Crusaders. Quickly, Apple Bloom ran up a large flight of spiral stairs to another glass room, but this one was filled with television monitors and had a long table with couches around it. Laying on one of the couches was the commander of a secret agency in Equestria that the princesses themselves had made, but only a select few ponies knew about it. These ponies included Agents Scootaloo (the inventor and one of the fastest flyers in Equestria), Sweetie Bell (the agent tasked with keeping full knowledge of the agency’s field records), and Apple Bloom (a field agent and medic when times needed, mostly armed with old family remedies).

Other ponies knew of the group of course, among them the six who recommended the members of it now, as well as the spirit of chaos and the pony in the blue box (well, he would know after his return home). At the head of this agency was their leader, one who had been the smallest of them all at one point. The gray-ish purple unicorn watched the monitors, her eyes never blinking as she scratched her blonde mane with her hoof.

“It’s done Dinky,” Apple Bloom said, smiling, “River’s back and we’re getting ready to send her home.”

“Good,” Dinky Hooves said as she stood, her muffin cutie mark showing until she pulled on her dark blue trench coat. “AB... Make sure to tell Spike to send off that letter, ok?”

“Which one boss?” the yellow mare asked.

“The one that says ‘Torchwhoof is back in business’.”
Doctor Whoof will return... In The Iron Horse...