Doctor Whooves Episode 11: Parents' Day

by Doctor Perseus

Rating: everyone
Tags: Doctor Whooves, Trixie, Spike, Adventure, Derpy Hooves, Crossover, Tragedy, Main 6, My Little Pony: Friendship is Magic, Human
Length: 13874

The Doctor heeds Applejack's request and has the TARDIS take them to July 6, 996, a day that changed Applejack's life forever.

The Doctor heeds to Applejack's request and has the TARDIS take them to July 6, 996. It quickly becomes apparent that Applejack has a plan to change a certain event that occurred on this day. But her choice to attempt to change her future could very well lead to the destruction of the entire universe.

Published 2013-01-26 10:50:02 UTC
Last updated 2013-01-26 10:50:02 UTC

Prologue

Doctor Whooves: Episode 11
Parents' Day

Prologue

Sweet Apple Acres, Ponyville, Equestria, Gaia, Summer, 996 C.E.

Applejack's muscles tensed as the TARDIS came to a surprisingly smooth stop. This was it. They had arrived. Applejack had thought about this ever since she began her adventures with the Doctor. Now it was a reality.

"And here we are!" said the Doctor with a smile. The suited stallion was a bit confused by Applejack's reaction. He expected her to smile or give off some form of happiness. But the only feeling he got from the earth pony was melancholy. The Doctor was beginning to become a little worried. Whatever this event was, it was apparent that it certainly wasn't something Applejack was happy about.

"Are you okay, Applejack?" Rainbow Dash asked as she approached her friend. Applejack remained silent. She turned towards the TARDIS doors and strolled out, leaving the others in an awkward silence.

Twilight was the first to exit the TARDIS after Applejack. The blue box had landed on top of a hill overlooking Sweet Apple Acres. It was early morning and the sun had just risen past the edge of the horizon. The air was surprisingly cool for a day in the middle of summer. Applejack was looking over the vast orchard. Her eyes scanned the trees until they came across the small farmhouse sitting off in the distance. It looked pretty much the same way it would look in 1002. Twilight looked out upon Sweet Apple Acres. Twilight felt strange. She had traveled into the past before but she had yet to visit Ponyville prior to her arrival there. The farm and orchard didn't look that different from what it would look like when Twilight would first arrive in Ponyville four years later, but there was one feature about the farm that stood out like a sore thumb. A little ways off from the main barn and farmhouse, there stood a tall, silver grain silo. It rose high into the sky, even surpassing the height of the barn.

"I don't remember that being there," Twilight stated as she pointed towards the grain silo.

"That's because it was...taken down before you arrived in Ponyville, Twilight," Applejack sighed. Twilight was puzzled. What was wrong with her friend? The others walked out of the TARDIS and the Doctor proceeded to close and lock the doors behind them.

"So what are we looking for?!" asked an excited Pinkie Pie. Once again, Applejack refused to answer the question. She simply gave another sigh before taking off down the hill. "Applejack! Wait!"

"What on earth is wrong with her?" Rarity asked.

"I wish I knew," said the Doctor.

The group followed Applejack until she came to a halt a little ways away from the farmhouse. A group of ponies were working outside. One of the ponies was instantly recognized as the younger, 16-year-old Big Macintosh who was heading out to begin plowing the fields. Granny Smith was sitting on the porch, rocking back and forth in her rocking chair.

"Make sure to come back for lunch, okay!" Granny Smith called to Big Mac.

"Eeyup!" Big Mac called back as he headed out into the fields.

"Applejack, what's going on?!" Rainbow hissed.

"I'll explain in a moment!" Applejack whispered back. Suddenly, the door to the farmhouse opened and out trotted the 13-year-old Applejack.

"I'm gonna go help Big Mac out in the field!" Applejack the younger called as she ran off after Big Mac.

"Okay but make sure to head into town later and pick up some vinegar for me!" called an unfamiliar, female voice from inside the house. Applejack bit down on her tongue at the sound of the voice. The voice was unfamiliar to everypony else in the group aside from Applejack. The sound of crying began emanating from inside the house. A mare walked out through the front door. She had an orange coat, a red mane, and a cutie mark that consisted of three apples: one red, one green, and one yellow. She was holding a crying, 1-year-old Apple Bloom in her arm. "It's okay, Apple Bloom! It's okay!"

"Do you need some help?" Granny Smith asked.

"I would appreciate that very much."

The mare handed Apple Bloom to Granny who proceeded to rock her back to sleep. The mare let out a great sigh as she sat down on the porch next to Granny's chair.

"I don't know where I'd be if you weren't here, Granny," the mare said with a smile.

"You'd be relying on my son most of the time," Granny snickered.

"You say that as if it's a bad thing," quipped a stallion who had just emerged from the doorway. He was a tall, muscular stallion with a light green coat similar to Granny's, a yellow mane, and a cutie mark that consisted of a single apple tree. "Celestia forbid that you get help from your husband every once in awhile!"

"Oh shut up, you," the mare teased as she stood up and kissed the stallion on the cheek. The stallion pulled away at the last second and began heading off towards the grain silo.

"Ah better hurry! Ah have to get a few bags of grain sorted out before ah go meet with the Mayor this afternoon!"

"No need to be a such a hurry, Johnny Apple!"

Johnny continued off towards the grain silo. The mare sighed as she sat back down on the porch.

"Why don't ya go help him, Emily?" Granny asked. "Y'all could use some alone time away from the baby."

"Maybe you're right. I'll go see if he needs any help with the grain. Maybe I could ask him out to go see one of the new films being shown at the theater. Would you mind looking over the farm tonight with Bic Mac and Applejack?"

"Don't worry. Ah don't mind."

"Thank you. You're a great mother-in-law."

Emily stood up and kissed Granny on the cheek before running after Johnny. Applejack stared out towards the field where her past self and Big Mac were working. She then turned towards the farmhouse where Granny was continuing to cradle the sleeping Apple Bloom. She lastly looked to see Johnny and Emily walking off towards the grain silo together.

"Okay, Applejack! I want answers now!" Rainbow snapped.

"What's happening today that's so important?" Trixie asked.

"And just who were that couple? I've never seen them before," said Pinkie. Applejack sighed as she turned back to face her friends.

She took in a deep breath before saying, "Johnny Apple and Emily Apple are their names. They're my parents...and...this is the day they died."

Deja Vu

Chapter 1: Deja Vu

Inside the TARDIS, Time Vortex, Unknown Place, Unknown Time

Rose Tyler leaned against the console. The Doctor sat silently in a nearby chair as he listened to her speak. She was talking about her father, Pete, who died tragically when she was only a baby. He could tell where this conversation was going but, still, he remained quiet and listened.

"So I was thinking, could we? Could we go and see my Dad...when he was still alive?" Rose asked.

"Where's this come from all of a sudden?" the Doctor asked.

"Alright then, if you can't. If it's against the laws of time or something, never mind. Just leave it."

"No, I can do anything. I'm just more worried about you."

"I wanna see him."

"Your wish is my command. But be careful what you wish for!"

The Doctor smiled as he stood up and approached the controls. He flipped a switch and the TARDIS began flying back through time.

Sweet Apple Acres, Ponyville, Equestria, Gaia, Summer, 996 C.E.

The Doctor felt a familiar, uneasy feeling rise in the pit of his stomach. This was all too familiar to him. He knew this event was important to Applejack and was even more sure that this particular event wasn't a happy one, but he surely wasn't expecting this. Everypony in the group fell silent. Applejack turned back towards the grain silo, watching sadly as her parents walked off together.

"Applejack...I'm so sorry," said Twilight.

"It's alright, Twilight. You don't have to be sorry. None of y'all needs to feel sorry," Applejack replied. Twilight felt bad. She had never given much thought to the topic of what happened to Applejack's parents. Applejack just seemed content enough with the family she had, and it certainly was a big family. The Doctor couldn't help but keep thinking about Rose. Rose and her father, Pete. This scenario just had too many similarities to Rose's situation.

"I hope you don't have any...drastic plans in mind," the Doctor said as he took a step forward.

"No. Ah don't. Ah just wanted to see them one last time."

Applejack began taking a few steps forward. Rainbow Dash quickly walked up to her and grabbed her shoulder.

"Where are you going?" she asked.

"I'm going to talk to my parents."

"I don't think that's a good idea," said Spike. "I mean. You don't look that different from your past self. Wouldn't your parents think it odd to see a future version of their daughter approaching them?"

"Ah guess you're right, Spike."

"She can use these," Trixie said as she handed her hat and cloak over to Applejack. "It's not much but I think you could use them to at least hide your face."

Applejack took the hat and cloak and put them on.

"I guess that works," said Derpy as she cocked her head and inverted her eyes a little bit.

"It's better than nothing," Fluttershy said with a smile.

"That's an odd look for you, Applejack!" Pinkie Pie exclaimed with a forced giggle.

"I don't think it goes with your coat and mane, though. Too polarizing," said Rarity.

"It's not permanent, ya know," Applejack said with a smile. She turned to Trixie and gave a slight nod. "Thank you, Trixie."

"Don't mention it," Trixie replied. Applejack then tipped the hat over her face and ran off towards her parents. The Doctor swallowed hard.

"I have a bad feeling about this," the Doctor admitted.

"Why is that?" Twilight asked.

"Bad memories."

Georgian Road, London, England, Earth, Autumn, 1987 A.D.

The Doctor and Rose stepped out of the TARDIS. The air was cool and breezy outside. The ship had parked in a small, concrete park situated between a patch of small trees and a road of apartments. Birds were chirping, music was emanating from a nearby radio, and the sound of children laughing could be heard in the distance. It was an average autumn day.

"It's so weird. The day my father died," Rose stated as a light breeze brushed against the strands of hair covering her face. "I thought it'd be sort of gloom and stormy. It's just an ordinary day."

"The past is another country. 1987's just the Isle of Wight," said the Doctor. "You're sure about this?"

"Yeah."

The Doctor and Rose quietly turned and walked around the bend. A series of apartment complexes stood across the street. A large, empty intersection stood in front of them. Rose began describing how her father died. The Doctor listened carefully. Pete had been late to a wedding and had gone to pick up a gift: a vase. He got out of his car and became victim of a hit and run. By the time the ambulance arrived, he was dead. He died alone, in the middle of that street. As Rose described the event to the Doctor, a small, green car pulled up and parked on the side of the road. Pete Tyler stepped out of the car. He was an average-sized man with a head of a light, red hair. He walked back to the back seat to grab the vase.

"Oh God, this is it," Rose sighed as a tan car came around the bend a little too quickly. The Doctor held onto Rose's hand tightly. Pete closed the door to the back seat and turned around just in time to see the car rushing towards him. Rose turned her head as the car collided with Pete Tyler's body.

Sweet Apple Acres, Ponyville, Equestria, Gaia, Summer, 996 C.E.

Applejack trotted across the farm towards the grain silo. Johnny and Emily Apple were talking casually as they opened it with a set of keys. Applejack's heart was pounding. This was it. She was going to talk to her parents again...only they couldn't know who she was. She lowered Trixie's hat over her face as she drew close to them.

"Excuse me," said Applejack, trying to make her voice as deep as possible. Johnny and Emily turned around. They were honestly a little bit surprised by the appearance of the mysterious mare in the starry, purple getup.

"Yes?" Johnny asked.

"Are you Johnny and Emily Apple by any chance?"

"That would be us. And who might you be?" Emily asked with a smile.

"Ah...I'm just a fan. I've heard so much about your farm from friends up in Canterlot. I just had to see where all those delicious apples came from!"

"So you're from Canterlot?" Johnny asked. "Funny. We don't get many ponies from Canterlot here in little old Ponyville that often."

"Well...I'm not from Canterlot. I'm a traveler."

"Well I can see that! I know a southern accent when I hear one!" Emily stated. "I may be from Manehattan but I've spent enough time around this husband of mine and his folk to know how to recognize it. I can even speak it myself."

"Really?"

"Yeah. I try not to though because I don't want to lose my old Manehattan roots. I've attempted to teach my children some old Manehattan lingo but none of them are interested. They'd just prefer talking like their father here."

"And is that a bad thing?" asked Johnny with a teasing smirk.

"I haven't decided yet. Maybe dear Apple Bloom will have more of an interest in learning about my side of the family."

"She'll need to have a lot of patience for that."

"Oh shut up, you!"

Johnny and Emily turned back towards Applejack and blushed.

"Oh look at us! Joking around and taking up your time!" Johnny said as he walked over to a nearby barrel of apples. He plucked one, shiny, red apple from the barrel and tossed it to Applejack. Applejack caught the apple while making sure to keep her hat over her face. "It's on the house. No need to pay for it."

"Thank you," said Applejack.

"Is something wrong with your face, ma'am? You're keeping that hat over most of your head," Emily stated.

"Uh...yeah. Ah got myself into a bad patch of berries. It's not pretty. Trust me!"

"Oh. I've been there before. Well ah hope you have a safe journey and, when you return to Canterlot, make sure to thank your friends there for promoting us!" Johnny said as he disappeared into the grain silo.

"I'll make sure to do that!"

"Good day," said Emily.

"Good day, Mrs. Apple."

Emily disappeared into the grain silo and shut the door behind her. Applejack kept the apple close to her as she trotted back to the place where the others were hiding.

"So...how did it go?" Rainbow asked as Applejack took the hat and cloak off.

"Good. Better than ah expected it to go," Applejack replied.

"Whatcha got there?" asked Pinkie as she saw the apple.

"An apple. My father just gave it to me for free."

"They look like they were really nice ponies," said Twilight.

"They were...and they are."

"So is everypony ready to head home?" the Doctor asked suddenly. He didn't mean to blurt the question out like that but the uneasy feeling in his stomach was causing him to become paranoid.

"Uh...sure," Trixie said as she put her hat and cloak back on.

"I hope you don't mind me asking...but how exactly did your parents die, Applejack?" Rarity asked.

"How about we all talk about it in the TARDIS?!" the Doctor asked.

"Okay! Okay! We're going!" said Spike.

"Is something wrong, Doctor?" Derpy asked.

"I just think we should get out of here before anything goes awry," the Doctor replied. Just then, a loud band rang through the air. Everypony turned to see that a large storm cloud had appeared out of nowhere, above the grain silo. A group of pegasi were attempting to keep the cloud under control. From the looks of things, something had caused the cloud to go out of control. Lightning bolts were shooting out of the cloud like bullets. But that wasn't the biggest problem. The grain silo was on fire! Applejack's muscles tightened again. All of the memories were flooding back to her.

Applejack the younger and Big Mac had stopped working and were running towards the grain silo. Granny Smith was sitting on the porch with Apple Bloom looking on at the burning tower in horror.

"Applejack! Big Mac! Stay away from there!" Granny yelled. Big Mac stayed but Applejack the younger kept running.

"Mom! Dad!" she cried. Big Mac was forced to grab his younger sister and hold her down.

"It's too dangerous!" he stated.

"But! Mom and Dad! Ah saw them go in there! They're inside, Big Mac! We have to save them!"

A part of the grain silo's roof caved in. A group of pegasi tried to ward off the storm cloud while others tried to douse the fire. It was no use. The fire was clearly out of control.

"Oh Celestia, this is it," Applejack the elder stated. She tried to look away but she couldn't. Her parents were dying and she had to stand there and deal with that fact...or did she? Applejack turned back towards the Doctor. The Doctor could only think of Rose when Applejack turned back to face him.

"Applejack," he said. "Don't you da-"

Applejack didn't stick around to listen. She turned around and broke into a run, heading straight for the burning grain silo. The apple she had received from her father fell to the ground in front of the Doctor with a soft thud. The Doctor's eyes widened and one of his hearts skipped a beat as he took off after the earth pony.

Out of the Fire and Into the Oven

Chapter 2: Out of the Fire and Into the Oven

Georgian Road, London, England, Earth, Autumn, 1987 A.D.

The Doctor and Rose looked around the corner at their past selves. Rose had frozen at the last second and had not rushed out to be with her father in his final moments. She wanted a second chance and the Doctor, while nervous, was willing to let Rose have one final shot at being with her father. Pete Tyler's green car pulled up and parked next to the sidewalk once again.

"I can't do this!" Rose stated.

"You don't have to do anything you don't want to but this is the last time we can be here," the Doctor said sadly. Rose watched as Pete stepped out of the car once again.

"Oh God, this is it," sighed Past Rose as the tan car swerved around the bend. At the last second, Rose broke into a run and ran towards Pete.

"Rose! No!" the Doctor cried but his warning fell upon deaf ears. The Past Doctor and Past Rose looked on in confusion as Rose ran past them. As Pete's eyes fell upon the car charging towards him, Rose grabbed him and pulled him to safety. The car drove past and Pete's vase fell to the ground with a light tap, not even breaking this time. The past versions of the Doctor and Rose disappeared in a quick flash of golden light as the Doctor looked on in horror.

Sweet Apple Acres, Ponyville, Equestria, Gaia, Summer, 996 C.E.

The Doctor tried to catch up to Applejack but the orange earth pony was proving to be much better at running than he was, which was surprising since he had done a great amount of running throughout his lifetime. She was already far ahead of him and growing close to reaching the burning grain silo.

"This is not good!" the Doctor said as he ran. "This is not good!"

Applejack's hat flew off her head and landed in front of the Doctor. The Doctor jumped over it and continued to chase after her.

Applejack the younger and Big Mac looked in confusion as the older Applejack and the Doctor ran towards the grain silo.

"Who are they?" asked Applejack the younger.

"I'm not sure," Big Mac replied. "I can't see them clearly from all the way over here."

Applejack finally made it to the grain silo. Smoke and fire was pouring out of the destroyed roof and the metal exterior was hotter than coals from a bonfire. Applejack turned around and kicked the door in with her hind legs. She walked inside and was greeted with stifling heat and toxic smoke. She could just hear the faint coughs of her parents from the other side of the interior of the silo.

"We...gotta...get out of here!" choked Emily.

"Ah...know! Where's the...door?!" Johnny coughed back. Applejack held her breath and charged into the smoky abyss. She found a wall of debris blocking her path and quickly knocked it aside. Johnny and Emily were slouched on the other side, their bodies nearly giving in to the toxic cloud around them. Flames were falling down from the ceiling and a wall of fire began to encircle them.

"Come on!" Applejack cried. "This way!"

Johnny and Emily stared at their savior. They were too exhausted and weak to determine who it was but they certainly had enough strength to stand up and follow them out of the fire. Applejack took hold of one of her mother's hooves and one of her father's hooves and led them out of the burning silo.

The Doctor had tried to charge in but two pegasi held him back.

"My friend just went in there!" he snapped.

"It's too dangerous!" said one of the pegasi. Suddenly, Applejack emerged from the fiery tower alongside her parents. She was covered in soot and her mane was a mess. No sooner had they exited the building, the entire thing collapsed with a loud scream. An explosion of fire, grain, and smoke rose into the sky, creating something that resembled a mushroom cloud. The Doctor's stomach sank. She had done it. She had saved her parents. She had doomed them all.

Georgian Road, London, England, Earth, Autumn, 1987 A.D.

The Doctor walked angrily down the sidewalk. He was still angry over the argument he had just had with Rose back in her father's apartment. She didn't understand what she had done. She could never understand. She was just another stupid ape. He reached the TARDIS and stopped. No...she wasn't that. She was just human. It was human for her to do that. A peculiar feeling dripped down his spine. He looked up at the sky. It looked cloudy and normal but something was definitely off about it. He shrugged the feeling off and opened the TARDIS doors. He looked on in horror at what he saw. There was nothing inside the TARDIS. The entire interior of the ship had disappeared. He knew what was wrong. They were coming.

"Rose!" the Doctor cried as he turned back and ran down the street towards the church.

Sweet Apple Acres, Ponyville, Equestria, Gaia, Summer, 996 C.E.

"Ah did it," said a shocked Applejack as she approached the Doctor. A pair of pegasi flew over and tended to the weakened Johnny and Emily. Applejack the younger and Big Mac ran forward and hugged their parents. Applejack looked back and couldn't help but smile. "Ah saved them."

She looked back to see that the Doctor was glaring at her. She didn't like that glare.

"Do you realize what you've just done?" he snapped.

"Yes! Ah just saved my parents' lives!"

"And at what cost?! There are two ponies alive here and now that shouldn't be!"

"Are you saying that my parents were better off burning alive in that grain silo?!"

Applejack was beginning to get angry.

"Everything happens for a reason, Applejack! Your parents were supposed to die in there! Was this your big plan this whole time? I could tell that you've been thinking about this ever since you and the others began traveling with me!" the Doctor snapped.

"It wasn't like this...at first. At first ah just wanted to go back and see them. Ah was ready to leave but then ah saw that grain silo catch fire and ah saw my past self running towards it. All the memories came rushing back all at once. Ah...ah just couldn't stand back and watch my parents die again!" Applejack snapped as tears rolled down her face. "You wouldn't understand."

"Don't you dare treat me like I'm the bad guy here! And don't you dare believe that I don't know how you feel! I've lost many friends and family, Applejack! My entire family was killed in the Last Great Time War, in which I was the only survivor! All of my kind...all of my family...were gone in a single instant of time. I've traveled with many beings from different walks of life. Eventually, they all left me. I've dealt with so much loss and live with so much guilt that any member of your species would burn up from the intensity of the feelings I have! I know what you've gone through! More than anypony else here!"

Applejack fell silent. The Doctor followed suit. He picked up Applejack's hat and dusted it off.

"I'm sorry for yelling. Here...take it," he said as he handed the hat to Applejack. Applejack took it and placed it on her head.

"Thank you," she replied. Applejack felt a tap on her shoulder and turned around to see her mother standing there.

"Are you the one who saved us?"

Applejack lowered her voice as she said, "Uh...yes."

"Thank you so much! My husband and I would have died if it weren't for you!"

"Really...it was no problem at all."

Applejack the younger walked forward and examined Applejack the elder's hat.

"Nice hat," she said. "It kind of looks like mine!"

"Does it now?"

"Thank you for saving my parents! Ah owe you one!"

"You owe something to me too," the Doctor said under his breath.

Twilight and the others were standing nearby.

"She actually saved them," said Twilight.

"Good for her," said Fluttershy with a smile.

"The Doctor doesn't look happy about it, though," said Derpy.

"Why not? Her parents are alive! What's the problem?! Is the universe going to get eaten up by monsters or something?" Spike asked. That's when a scream of terror emanating from right above them.

Outside St. Markus Church, London, England, Earth, Autumn, 1987 C.E.

Rose had ridden to the church with Pete and it didn't take long for her mum, Jackie, to assume that the older Rose was another one of Pete's mistresses. Pete and Jackie, after shouting to each other, began to calmly talk out their disagreements. The sight of her parents making up made Rose smile a little bit. Suddenly, a young, black boy ran around the corner towards the church.

"Monsters! Going to eat us!" he cried as he ran.

"What sort of monsters, sweetheart?" asked one of the bride's friends.

"It's aliens!"

The women simply giggled as the boy ran into the church. Rose quickly recognized the boy as the past version of her boyfriend, Mickey Smith. Then she heard a familiar voice.

"Rose!" called the voice. It was the Doctor. Rose smiled as she turned around. He was running towards her quickly. Something appeared to be wrong. "Get in the church!"

Rose looked up just in time to see a brown creature materialize out of thin air. It had a body that resembled a mix between a bat, an insect, and a squid. It stretched out its arms to reveal a large, gaping mouth hiding behind them. Rose screamed as the creature flew towards her.

Sweet Apple Acres, Ponyville, Equestria, Gaia, Summer, 996 C.E.

Twilight looked up to see a brown creature shoving a screaming pegasus mare into its gaping mouth.

"What in Celestia's name is that?!" Rarity cried. The creature looked down and flew towards the group. Several more creatures began materializing out of thin air. Twilight and Derpy ran towards the Doctor.

"Doctor! What are they?!" Twilight asked.

"Reapers!" the Doctor replied.

"What do they want?" Derpy asked.

"Food."

"I have a bad feeling about what the food is."

The Doctor looked around. There had to be a place to hide from the Reapers here. Sadly, there were no churches in Equestria. Then his eyes fell across the barn. It was a shot in the dark but it would have to do for now.

"Everypony in the barn!" the Doctor ordered. Everypony followed suit. Granny opened the barn door and let everypony run inside. A Reaper bore down towards Fluttershy, who had tripped over of jagged root.

"Get away from her!" Trixie snapped. Trixie fired a blast of magic at the Reaper. It had no effect. "Fluttershy! Run!"

Fluttershy got up and ran for the barn. She looked back just in time to see Trixie get devoured by the Reaper.

"Trixie!" Fluttershy cried. The Reaper charged for her but the Doctor appeared and threw a trash can lid at the creature.

"Keep moving!" he ordered. Everypony else made it safely into the barn. As Applejack passed by Granny, who was holding the doors open, the elderly mare handed the infant Apple Bloom to her.

"Give her to my son," she said.

"Granny Smith," Applejack said sadly. The Doctor and Fluttershy came up from behind and shoved Applejack into the barn. Granny was about to enter the barn and shut the doors when a Reaper grabbed her from behind.

"Granny Smith!" cried Applejack the younger. The Reapers tried to barge through the doors but the Doctor and Big Mac proceeded to close and lock the doors. The Reapers cried as they clawed against the exterior of the barn.

"M...mother," Johnny said sadly.

"Trixie," Fluttershy croaked.

The Doctor turned to Applejack the elder and whispered, "This is why you don't change history."

The Paradox

Chapter 3: The Paradox

Outside St. Markus Church, London, England, Earth, Autumn, 1987 A.D.

The Doctor pushed Rose out of the way just in time. The Reaper flew over them and prepared to dive down again.

"Get in the church!" the Doctor ordered as he helped Rose up. The others ran for the church only to see several more Reapers materialize in front of them.

"Oh my God! What are they?! WHAT ARE THEY?!" screamed one of the bride's friends.

The Doctor pointed towards the church and yelled, "Inside!"

The groom ran out of the church and tried to reach his bride but the Doctor told him to remain inside. The groom's father tried to run but one of the Reapers swooped down and devoured him. The bride screamed as a Reaper flew towards her but, at the last second, the Reaper turned and devoured the Minister.

"Get inside!" the Doctor ordered as everyone ran for the church. Once everybody was inside, the Doctor closed and locked the doors. The Reapers fell silent as they proceeded to begin flying around the church. There was no way out. The Doctor, Rose, and the others were trapped.

Sweet Apple Acres, Ponyville, Equestria, Gaia, Summer, 996 C.E.

Everypony was shaken up from what had just happened. The only ones who had made it inside the barn were the Doctor, Twilight, Derpy, Spike, Applejack the elder, Applejack the younger, Rainbow Dash, Pinkie Pie, Fluttershy, Rarity, Johnny, Emily, Big Mac, the infant Apple Bloom, and a pegasus mare named Sarah. All of the others, including Trixie and Granny Smith, had fallen victim to the Reapers.

"Mother," Johnny cried as he leaned up against Emily.

"First the fire and now this," Emily sighed as she held her husband close. Applejack the elder was sitting in a corner of the barn by herself. She listened as the Reapers occasionally screamed, as if yelling at them to come out. The Doctor was talking with Twilight and Derpy while the others were making sure that the barn was secure enough to prevent the Reapers from breaking in.

"So...what are Reapers exactly?" asked Twilight.

"Creatures from another dimension. The sterilization of time," the Doctor replied.

"What does that mean?" Derpy asked.

"Paradoxes are odd things. When they occur, numerous things can happen. Back in my universe, when the Time Lords were still alive, they would help heal the time stream if a paradox were to occur. But, with them gone, the effects of paradoxes became...varied and long-lasting. That's where the Reapers come in. They're creatures linked to time itself. A paradox can be described as a wound in time and Reapers are like the antibodies of time. They come to sterilize the wound."

"Let me guess, by eating everything in sight," Twilight sighed.

"Yes."

"Doctor...are Trixie and Granny Smith...dead?" Derpy croaked.

"Not necessarily. If we find a way to defeat the Reapers, then they should return."

"But how are we to defeat them?"

"Nothing in the universe can destroy them...but there is one way."

"And that is?" Twilight asked.

"Heh...you know. Reapers are kind of like the polar opposites of Weeping Angels."

"Huh?"

"You see, paradoxes are poisonous to Weeping Angels, due to their primary food source being stable, linear, potential time energy. Paradoxes are what give Reapers power. If we somehow found a way to mend the wound, by getting rid of the paradox, then the Reapers would die."

"Paradoxes are poisonous to Weeping Angels and are power to Reapers. Interesting."

"But how are we to mend the paradox? What is the paradox anyway?" Derpy asked.

"Ah think we all know what it is," Applejack sighed as she looked over at her parents. The Doctor turned to Applejack and sat down next to her. "Ah didn't mean for all of this to happen."

"I know you meant well, Applejack. It was only human for you do that," the Doctor said.

"Human? What's that supposed to mean?"

The Doctor chuckled and smiled as he looked at Applejack.

"You know, you ponies seem to resemble humans more and more. Similar morals, similar beliefs, a similar stand on what's right and wrong, and even similar amounts of stubborn holiness. Brilliant you are. Both of you."

"What are you talking about, Doctor?"

"Sorry...just reliving old memories. I had a friend who did the exact same thing that you just did, Applejack."

"Was it Rose?" Twilight asked. "I remember you telling me that story about her and her father back when we visited the Castle of Equestria."

"You have a good memory, Twilight Sparkle. Almost as good as mine!"

"I know."

Twilight gave a forced smile which caused Derpy to giggle.

"So you've encountered the Reapers before?" Applejack asked.

"Yes. The last encounter wasn't fun. I was devoured," the Doctor replied.

"How did it all end? How were the Reapers defeated?"

"You see, Rose saved her father from dying. This allowed the Reapers to enter our universe. Her father was originally run over by a car (it's a human contraption and I'll explain more about it later) and that same car kept popping up out of nowhere. Pete, Rose's father, ran out and let himself get hit by the car. Thus the timeline was restored."

"So...are you saying that...in order for the Reapers to go away...my parents have to burn to death?"

"Sadly...yes."

Applejack lowered her head. She shook it before lifting it up again.

"Ah remember how everything originally played out. The fire was out of control and ah was horrified. Ah wanted to run in and save them but Big Mac held me down to keep me safe. Nopony ran in to save them. Somepony should have tried to save them. That's what made it all the worse when ah found out what had happened to them. Ah guess...that's another reason why ah saved them. Just so that somepony could be there to try and save them. So that my past self didn't feel that her parents, my parents, our parents died without any original chance of surviving in the first place."

She lowered her head again and wept. Her coat was still covered in soot and her mane was still messy. Rainbow Dash flew down and threw a towel at her.

"You might want to clean yourself off," chuckled the cyan pegasus.

"Well the soot acts as a somewhat useful disguise to prevent her family from recognizing her," said Derpy. "The last thing we need right now is more confusion amongst ourselves."

Applejack took the towel and pushed it aside. The Reapers screamed again. The Doctor looked through a crack in the wall, expecting to see a ghostly grain silo burning in the distance but...he saw nothing of the sort.

"That's strange," he said to himself as he backed up from the wall.

"What are we to do now?" Applejack the younger asked her parents.

"Ah don't know, sugarcube. Don't worry. We'll think of something!" Johnny replied. Emily knelt down and hugged her daughter.

"Listen to me, Applejack. Whatever happens, never forget that your father and I love you, Big Mac, and Apple Bloom with all our hearts. Never forget that!" she said.

"Ah won't, Momma," said Applejack the younger as she hugged her mother back. Applejack the younger turned towards her future self, her parents' savior, and began approaching her. The Doctor's heart skipped a beat. Normally a past and future self interacting with each other wouldn't be that catastrophic, but when there was a paradox going on and an army of Reapers was present that tends to make things more dangerous. Applejack the elder was sitting with her head drooped. Applejack the younger reached out one of her hooves. "Hey, are you okay?"

"Applejack! Don't touch her!" the Doctor yelled.

St. Markus Church, London, England, Earth, Autumn, 1987 A.D.

Rose sat silently as the the golden outline of the TARDIS slowly materialized in the center of the church. The Doctor was going to fix everything. She knew it. He was going to send the Reapers away, all of the people who died would return, and her father would remain alive. And, now, her father knew who she was. The Doctor sat next to Rose in silence.

Rose leaned in to the Doctor and asked, "When time gets sorted out-"

"Everybody here forgets what happened," the Doctor interrupted. "And don't worry. The thing you changed will stay changed."

"You mean I'll still be alive?" Pete Tyler asked. "Though, I'm meant to be dead. That's why I haven't done anything with my life. Why it didn't mean anything."

"It doesn't work like that."

"Rubbish. I was so useless I couldn't even die properly! Now it's my fault all of this has happened."

"This is my fault!" Rose argued.

"No, love. I'm your dad. It's my job for it to be my fault."

Suddenly, Jackie approached them with baby Rose in her arms. She asked, "Her dad? How are you her dad?! How old were you?! Twelve?! Oh, that's disgusting!"

The Doctor rolled his eyes as he stood up and walked a few feet away.

"Jacks, listen. This is Rose," Pete said as he stood up.

"Rose?! How sick is that?! You give my daughter a second-hand name! How many are there?! Did you call them all Rose?!"

"Oh, for God's sake, look! It's the same Rose!"

Pete took the infant Rose and began handing it to the older Rose.

"Rose!" cried the Doctor as he ran for her.

Sweet Apple Acres, Ponyville, Equestria, Gaia, Summer, 996 C.E.

Applejack the elder looked up as her younger self placed a hoof on her shoulder. A flash of golden light exploded from where the two Applejacks were situated. A Reaper materialized in the middle of the barn.

St. Markus Church, London, England, Earth, Autumn, 1987 A.D.

Rose held her infant self tightly in her arms. A flash of golden light exploded from where the two Roses were situated. A Reaper materialized in the middle of the church.

Sweet Apple Acres, Ponyville, Equestria, Gaia, Summer, 996 C.E.

"Everypony get behind me!" the Doctor screamed as the Reaper stared down at them angrily.

"Applejack! What's happened to Applejack?!" Emily cried. The Doctor looked to where the two Applejacks were and nearly fainted from shock. Standing before him was a young, blonde girl in her late teens holding an infant wrapped comfortably in her arms. The girl looked around the barn with a mix of shock and surprise.

"Where am I?!" asked Rose Tyler. She looked at the chestnut, suited stallion before her. "Who are you?! What are you?! A horse?!"

The Doctor slowly approached Rose as the Reaper screamed from overhead. He said, "Rose...it's me. I'm the Doctor."

St. Markus Church, London, England, Earth, Autumn, 1987 A.D.

"Everybody get behind me!" the Doctor ordered as the Reaper stared down at them all hungrily.

"Where's Rose? What's happened to Rose?!" Pete asked. The Doctor looked and was surprised by what he saw. Standing before him was a pair of orange, female ponies with blonde manes. One was wearing a hat and was covered in soot.

"What happened?! Where are we?!" asked the 13-year-old Applejack. Jackie fainted at the sight of the pony before her speaking. The 19-year-old Applejack looked at the Doctor standing before her. She had never seen a human being before and didn't know what to think.

"Who are you?! What are you?!" Applejack the elder asked in shock. The Doctor awkwardly approached Applejack as the Reaper screamed from overhead.

"I'm the Doctor and I could ask you the same question," he replied.

The Merging Begins

Chapter 4: The Merging Begins

Sweet Apple Acres, Ponyville, Equestria, Gaia, Summer, 996 C.E.

"What?!" asked the still surprised Rose. The Reaper screamed again and flew down towards them.

"Duck!" Derpy warned. Everypony heeded the warning and dropped to the ground as the Reaper proceeded to fly over them. Rose held onto her younger self tightly as the Reaper flew back down towards them. She didn't know what was going on or where she had been transported to but she knew that the Reapers were an apparent danger to her, no matter when or where she ended up. The Doctor grabbed onto Rose's hand and helped her up.

"How are we supposed to defeat that thing?!" Johnny asked.

"I don't know! But it's coming back!" Twilight cried. The Reaper screeched again as it flew back down. Suddenly, a ball of fire appeared out of nowhere and smashed into the Reaper. It didn't cause much damage but it did make the creature dizzy for a moment.

"Where on earth did that come from?!" Rarity asked. That's when a series of fireballs began falling from the ceiling, out of thin air. The barn began to bend and twist as if its walls were made of flexible plastic and were being bent by a giant. For a second, Rose could swear that she could see the interior of the church she had previously been in. Shadowy figures began appearing all around them and even the Reaper was beginning to become slightly confused.

"What's happening?!" Fluttershy asked.

"Those are some pretty colors!" Pinkie exclaimed as she pointed towards the ceiling. The colors of the barn were beginning to mix with a layer of colors that seemed to be coming from a window of colored glass. The Doctor then noticed a familiar object in the distance. In the vision of the ghostly church, he could see his Sonic Screwdriver perched inside a golden outline of the TARDIS. He pulled out his own Sonic Screwdriver and, with a shrug of his shoulders, aimed it at the ghostly Screwdriver and fired. A loud, sonic sound began reverberating throughout the barn and the Reaper began to scream. The ghostly church began to disappear. Another shadowy figure, flying in the air within the vision of the church, flew towards the Reaper. The Reaper flew towards the shadow and they both exploded in a fiery cloud of golden ashes. The ashes fell to the ground and disappeared into nothing. For a second afterwards, Johnny and Emily swore that they could see the interior of the burning grain silo. Then the vision disappeared, leaving both of them bewildered and confused.

"What was that?!" Rainbow Dash asked.

"Where's my sister and that dirty mare?" Big Mac asked.

"And who are they?" asked Sarah the pegasus. Rose was still in shock. She continued to hold her past self tightly as the group of ponies approached her.

"W...where am I?" Rose asked.

"You're in Equestria, Rose. Circa 996," the Doctor replied. "I'm the Doctor."

"You can't be the Doctor. The Doctor's an alien who looks like a human! You're a-"

"An alien who looks like a pony but once looked like a human. I know this is a lot to take in, Rose, but I am the Doctor. I may not look like your Doctor but I am a future version of him."

"Prove it."

"Okay then, if you insist. You're Rose Tyler. Born in 1986. Hometown is London, England. Your mother's name is Jaqueline "Jackie" Tyler and your father's name is Pete Tyler but he died in 1987 due to being hit by a car on his way to the wedding of Stuart Hoskins and Sarah Clarke. My ship is called the TARDIS, which stands for Time and Relative Dimension in Space. I met you in 2005 when you ran into an army of Autons in the department store in which you worked. Henrik's I believe is what it was called. We helped save your boyfriend, Mickey Smith, from the Autons and that's when you began your travels with me. If I have your current place in my timeline correct then so far you've seen the death of Earth, met Charles Dickens, saved London from the Slitheen family, met a Dalek below Utah in 2012, and have traveled to the year 200,000 to save Satellite 5 from the Editor...and that's all the major events that I recount from the top of my head."

Rose stood there in shocked silence. She couldn't believe it. Somehow, someway, the pony in the blue suit standing before her was indeed the Doctor. Rose approached the Doctor and knelt down, staring deeply into his eyes in the process. The Doctor smiled and took one of Rose's hands in one of his hooves.

"I remember when you asked me why I had a northern accent if I were an alien," he chuckled. "And I remember saying, "Lots of planets have a north," in response. Do you remember that?"

"Yes," Rose said with a laugh. "I remember." Rose then reached forward and gave the Doctor a hug. The Doctor happily hugged her back. Twilight and Derpy looked at each other awkwardly and then turned back to the Doctor and Rose. "It's you! I can't believe it's really you!"

"I could easily say the same thing."

Rose stepped back from the Doctor and stood up. Johnny was the first to step forward.

"I'm glad that you two have reunited but my daughter just disappeared in a flash of golden light. Ah would be very happy to know exactly where she's gone off to," he stated.

"Right!" the Doctor exclaimed. He turned towards Twilight, Derpy, and the others and beckoned them over. "Let me discuss this with my group in private for a moment!"

The Doctor huddled in a group with Twilight, Derpy, Spike, Rainbow Dash, Pinkie Pie, Fluttershy, and Rarity. Rose stood quietly in the center of the barn, continuing to keep her infant self calm and collected.

"So what exactly just happened?" Rainbow Dash asked.

"It's hard to say exactly but I think I have an idea," said the Doctor.

"Well spit it out then!" exclaimed Pinkie.

"We're all ears," Spike added.

"Okay. I believe our two paradoxes have somehow managed to cross paths," the Doctor replied.

"Two paradoxes? I thought there was only one paradox," said Rarity.

"He's talking about Rose's," said Twilight and Derpy together.

"Thank you, you two!" the Doctor said happily. Twilight and Derpy blushed slightly and turned away from each other.

"Rose is in a paradox too?" Fluttershy asked.

"Yes. I've already told Twilight and Derpy this story but, several years ago when I was traveling with Rose, I took her back to see her father who had died when she was a baby. She saved his life and thus a paradox was created and the Reapers were able to enter our universe. The same situation has happened here with Applejack saving her parents. I don't know how or why but our two paradoxes, taking place in different dimensions and times, and somehow managed to collide. Now, if my theory is correct, if Rose and her infant self are here then that means Applejack and her younger self are in the church where my younger self is."

"So...we're basically dealing with a paradox within a paradox," Spike guessed.

"Pretty much."

"Come on!" Rainbow Dash groaned. "We just had to deal with the Weeping Angels and their freaky, never-ending paradox and now we have to deal with these Reapers and two paradoxes?!"

"Yeah."

"Why can we ever face a small problem? Why do problems involving you have to be freaking ginormous?!"

"I've dealt with problems like this throughout the nine centuries of my existence and I'm still not able to answer that question with a satisfactory answer."

"I guess it's kind of like whether or not we'll ever find out what your name is," Fluttershy said with a smile. "It'll always be one of those unanswerable questions."

"Anyway, moving on, from what we just saw it's safe to assume that our two timelines are merging."

"That really doesn't sound good," said Twilight.

"I don't think it is," Derpy added.

"It's not, in the long run. At first, everything will be fine. This barn and the church will probably just exist in one place of time and space. Then the true merging will commence and time itself will collapse."

"Lovely," said Rarity sarcastically.

"This whole thing is odd, though."

"I think I would describe this crisis as more than being odd, Doctor," said Twilight.

"I know that but my past self is experiencing this too...and I don't remember any of it."

"You don't?" Pinkie asked.

"No. Well, I don't remember much because I was devoured by a Reaper but I definitely don't remember the two Roses disappearing and the two Applejacks appearing in their place. I would remember that."

"More paradox mumbo jumbo probably," Derpy guessed.

"Perhaps."

As the Doctor and the others continued their discussion, Rose went off and sat by herself in a corner of the barn. She could hear the Reapers screaming outside. She looked towards Johnny, Emily, and Big Mac to see that they were incredibly worried. She had no idea who Applejack was but it was apparent that she meant a lot to them. She turned back to the group of huddled ponies and chuckled at the sight of Spike the dragon.

"Oh, Doctor. Of all the worlds to end up in, you just had to go for the weirdest," she sighed. She still couldn't believe that the Doctor she knew and traveled with was going to eventually become a chestnut stallion with a brown mane and a blue suit. Change was certainly strange sometimes. She leaned back against one of the barn's support posts and sighed. "I wonder what my Doctor's doing right now."

St. Markus Church, London, England, Earth, Autumn, 1987 A.D.

The Doctor had taken the two Applejacks to a corner of the church to discuss the current situation with them. Following the weird vision of the barn and the disappearance of the two Roses and the Reaper, the Doctor had a lot to discuss with the two mares.

"I really don't know what to ask first," the Doctor sighed as he buried his face in his hands. "I guess I should start off by asking where Rose is."

"Rose?" Applejack the elder asked.

"We don't know any Rose," Applejack the younger replied. This was a lie. Applejack's younger self may not have heard of any Rose but Applejack the elder certainly did.

"Ah do."

"So you know where Rose has ended up?" the Doctor asked.

"No...I'm not entirely sure about that. Ah just know who you're talking about."

"How? How do you know Rose?"

"Ah don't know her on a personal level but, if you are the Doctor, then you've told me about her before...or are going to tell me about her."

"What are you talking about?"

"Let's just say that I'm traveling around with your future self and you've told me about this whole event before. You told me how you took Rose back in time to see her father, only for it to end up with Rose saving her father's life and causing a paradox which let the Reapers appear."

"Huh. I guess you do know me. It looks like I'm going to be keeping some very odd company in the future."

"What's that supposed to mean?!"

"Nothing! Nothing! So, from how things look, I can only determine that you and my future self are dealing with a paradox of your own."

"You could say that."

"And how did this paradox come about?"

"Ah-"

Applejack stopped. She looked at her younger self. She couldn't bear to say it. How could she say to her younger self that her parents were supposed to die that day and that their continued existence is what was causing the paradox and the presence of the Reapers in the first place?

"Let's just say that somepony prevented a certain...event from occurring."

"Somepony? What world are you from anyway?"

"Equestria. It's a country on the planet Gaia. What world is this, anyway?"

"You're in England. It's a country on the planet Earth."

"I'm guessing this is where humans come from."

"Yes."

"What about you? Where does your species come from, again? Ah don't think your future self has told me that particular detail yet."

"Gallifrey. That's my...that was my planet's name."

"What happened to it?"

"It got destroyed in the Last Great Time War."

Applejack remembered her Doctor mentioning the Last Great Time War when he was reading her the riot act back in Ponyville. She obviously didn't know much about it but it was pretty clear to her that this was pretty devastating to the Doctor in many ways.

"So how are we to get back home and how are we supposed to get rid of those...things?" asked Applejack the younger.

"They're called Reapers," Applejack the elder corrected.

"Ah don't care what they're called! They're threatening the lives of my family and me! Ah nearly lost my parents earlier today in that grain silo! Ah don't want to lose them from a group of winged varmints!"

"You don't know the half of it."

Applejack made sure to say that last statement under her breath. The Doctor looked and noticed that Jackie was finally starting to come to and she quickly realized that her baby Rose was missing. That's when the building shook again and a shady vision of the barn appeared for a brief moment before vanishing again.

"It looks like we don't have much time before our two timelines interconnect," said the Doctor.

"Sure looks like it," Applejack the elder added. Suddenly, another ghostly image appeared but it wasn't of the barn this time. It was a vision of the church a few minutes previously. The vision quickly disappeared.

"What was that?" Applejack the younger asked.

"It seems that different times in this timestream are beginning to connect. This isn't good. The Reapers are growing stronger as we speak and we have two paradoxes slowly drawing closer and closer together. If these two paradoxes manage to merge completely then we can just say goodbye to our bodies because we'll all be torn apart: atom by atom," said the Doctor.

"Ah really hope that doesn't happen," Applejack the elder croaked. The building shook again, only this time it was much more violent. Half of the church began to disappear and was beginning to be replaced by the interior of a barn. Shadowy figures were walking around in this barn segment but were progressively become more and more solid with each passing second.

"Too bad...because it looks like it's started."

Daughters from the Future

Chapter 5: Daughters from the Future

Sweet Apple Acres/St. Markus Church, Ponyville/London, Equestria/England, Gaia/Earth, Summer/Autumn, 996 C.E./1987 A.D.

The Doctor watched as the other half of the barn slowly began to fade away and was instantly replaced with half of the St. Markus Church. The barn/church stopped shaking and everypony and everyone fell silent.

"Mom! Dad!" cried Applejack the younger as she ran over to her parents. Johnny and Emily hugged Applejack tightly. The people from the wedding were in shock from what they were seeing.

"More of them?!" Jackie asked.

"Apparently so," said the past, humanoid Doctor. The present, ponified Doctor approached his past self awkwardly.

"It's always strange when I meet myself," the Present Doctor stated. The Past Doctor stared at the Present Doctor.

"Wait...so...are you-"

"Yeah. I'm you...two regenerations later."

"I see. I'm going to become a horse."

The Past Doctor laughed gleefully as he turned to Rose.

"Hey, Rose!" he laughed. "I'm going to become a horse!"

"I figured that much out," Rose replied with a chuckle. Jackie walked over into the barn half and took baby Rose from older Rose's arms.

"You're lucky my little Rose isn't hurt!" she snapped before walking back into the church half. Rose rolled her eyes and smiled. She would find out the truth soon enough. Applejack walked forward and looked at her younger self standing with her parents. She wanted them to know so badly. She wanted to tell them who she really was.

"So now what?" Rainbow Dash asked. The Reapers screamed from outside.

"I'd say that we're in quite a pickle," Rarity replied.

"I'm not in the mood for pickles right now," Pinkie Pie added.

"How is anypony supposed to respond to that?" Spike asked.

"I'm going to pick some very, VERY odd company in my future," said the Past Doctor.

"You'll get used to them...for the most part," said the Present Doctor as he stared at Pinkie Pie. Applejack and Rose caught each other's eyes.

"So you're Rose," she said.

"And I'm guessing that you're Applejack," said Rose.

"Guilty as charged."

"So you've created a paradox of your own?"

"Yeah."

Applejack looked over at her parents. Rose glanced back at Johnny and Emily before turning back to Applejack.

"I see," Rose continued. "Couldn't resist trying to change the future, huh?"

"Ah just couldn't stand there and watch my parents die," Applejack replied.

"I know how you feel. I felt the same way when I saw my dad about to get hit by that car."

Applejack turned back to look at Pete, who was standing with Jackie and looking at baby Rose.

"Does he...know who you are?" Applejack asked.

"Yeah...I told him," Rose replied. "My mum doesn't know yet. Do your parents know?"

"No. Neither of them do."

"All of time and space could be destroyed at any moment. I think it would be best for my mum to know who I am. Maybe your parents should know the secret too."

"Ah guess."

"Do you want them to know?"

Suddenly, the lights outside began to dim and the interior of the barn/church began to darken.

Applejack stared at Rose and said, "Yes. More than anything at the moment."

"Then go tell them," Rose said. Rose patted Applejack on the shoulder before walking over to speak with her mother. Applejack cleared her throat and began walking over to her parents. The Present Doctor watched quietly from a distance.

Johnny and Emily were busy comforting the younger Applejack and Big Mac, who was holding the infant Apple Bloom.

"Are we...are we gonna die?" asked Applejack the younger. Johnny and Emily didn't know what was going to happen. Applejack the elder approached them.

"It's you again," said Johnny with a small smile. "How are ya holding up?"

"Alright. All of time and space is about to get destroyed so I'm not feeling completely spectacular," replied Applejack. Johnny chuckled.

"Is there something on your mind?" Emily asked. "You look like you want to say something."

Applejack heard a gasp and looked over her shoulder to see Jackie and Pete hugging the older Rose. She must have told her mother who she really was.

"Ah do have something to tell you," said Applejack as she turned around. She looked at a towel lying on a table nearby. It was the rag that Rainbow Dash had given her earlier. "Can you hand me that rag?"

"Sure."

Emily retrieved the rag and handed it to Applejack. Applejack sighed as she wiped the soot off her coat. She dusted off her mane and got as much of the grim off of her body as she could. By the end, she was still dirty but she was definitely identifiable. Applejack the younger's eyes widened. She looked back at her cutie mark and then looked at Applejack the elder's cutie mark.

"You...you have my cutie mark," she said.

"Ah do," said Applejack.

"You look so familiar," said Johnny.

"Take a close look. Who do you think ah am?"

Johnny and Emily looked closely at Applejack. A couple minutes of silence followed. Then, their eyes widened. They looked at their Applejack and then looked at the future Applejack.

"It...can't...be," Emily exclaimed.

"Impossible!" Johnny breathed.

Big Mac stared and asked, "Are...are you-"

"Me?" croaked Applejack the younger. Applejack could feel her eyes watering up. She couldn't speak. All she could do was give a simple nod. Emily walked forward and looked deep into Applejack's eyes.

"Your eyes. Those...those are my daughter's eyes! My Applejack's eyes! My Applejack's eyes!" Emily cried and she held Applejack tightly in her arms. Johnny walked forward and followed suit. Applejack let the tears fall from her eyes. Applejack the younger and Big Mac could only stand there in stunned silence. Apple Bloom snoozed comfortably in one of Big Mac's arms. Applejack wiped the tears from her eyes as she broke away from her parents' grasp.

"But how?!" asked Johnny.

"The Doctor's a time traveler. Ah recently hitched a ride," Applejack replied.

"Time travel. After all this, ah wouldn't doubt anything."

"This is all my fault!"

"What? How is this your fault?" Emily asked. Applejack looked at her younger self and Big Mac. She wanted to cry again.

"The Reapers came because of a paradox that ah caused."

"How did you cause it?"

Applejack couldn't say it. All she could do was stare sadly at her parents. Johnny and Emily looked and their daughter from the future and then looked at themselves. It didn't take them long to put everything together.

"We...weren't supposed to come out of that grain silo...were we?" Johnny asked. Applejack couldn't respond to that. She simply lowered her head.

"What do you mean by that?" asked Applejack the younger. Applejack the elder felt a pat on her shoulder. She looked up to see that it was the Doctor, her Doctor.

"We shouldn't be here. That's why this has happened," said Emily. The Doctor, like Applejack, turned to face Applejack the younger and Big Mac.

"I'm sorry. I'm so, so sorry," he said. "But...it's true."

Emily lowered her head and began to cry. Suddenly, she felt the air get warm around her. She looked up to see a towering inferno before her. She screamed and the inferno vanished.

"Emily?! What's wrong?!" Johnny asked.

"Did...did you see it?" she asked. Johnny looked and he too saw the inferno for a few seconds. It disappeared soon after he saw it. "What was that?!"

The Doctor and Applejack turned to each other. The Doctor could only sigh.

Rose walked back over to her Doctor.

"Had a good talk with your parents?" he asked.

"Yeah. It looks like we're stuck," she replied.

"I guess we are. It was a great ride: traveling with you, Rose Tyler."

"The feeling is mutual, Doctor."

"We shouldn't be giving up just yet!" exclaimed Derpy, who approached them. "You're the Doctor, right? The Doctor from the past?"

"I guess so," the Past Doctor replied.

"You can think of something to save us! I know you can!"

"What's your name?"

"Derpy. Derpy Hooves."

"Interesting name. Well, Derpy, I just don't know. We're really caught up the creek without a paddle."

"Well we have two paradoxes to deal with. Maybe we need the combined minds of two Doctors to get out of this mess!"

"Two Doctors working together? Sounds interesting," said Rose.

"It's happened before and it's led to quite the fireworks display," Twilight chuckled as she walked forward.

"Are you all talking about me with my past self and all behind my back, no less?" asked the Present Doctor as he approached them.

"Maybe," Derpy teased.

"You all seem chipper about this whole situation."

"Do you have any plans on how to defeat these paradoxes?" Rose asked.

"I have a plan but it's not going to have positive results for one human and two ponies here."

"So what's the plan?" Twilight asked.

"I can already guess what you're thinking of," said the Past Doctor.

"Yes...and do you like it?"

"No...but it's the only way."

"I feel the same way, friend."

"What are you two talking about?" asked Derpy.

"The way to defeat the paradoxes!" said the two Doctors together.

"This is starting to get too weird for me," said Rose.

The two Doctor stared at each other and nodded their heads as they simultaneously said, "Yeah."

"Will you two stop doing that?!" asked Twilight, Derpy, and Rose together.

"Only if you do," the Doctors replied. The three companions groaned.

"I wonder what's outside," said the Present Doctor.

"The Reapers. What else would be out there?" Twilight asked.

"Our last chance at restoring our respective timelines!"

The Doctor rushed towards the barn door/church door. He opened them to find himself staring out into neither Sweet Apple Acres nor London but an endless, black void full of Reapers. Below the barn/church there burned a ball of fire the size of the Earth. A Reaper flew towards the door and the Doctor was quick to close it.

"Great. There's nothing left except fire and darkness," the Doctor said. "That means we don't have much time left on our hands or our hooves!"

"I wish there were another way," said the Past Doctor.

"Me too, but there's no other way to fix this."

"So you've got a plan?" asked a familiar voice. The Doctors looked to see that Applejack, Johnny, Emily, and Pete were standing before them.

"Yeah...but you're not going to like it," said the Past Doctor.

"Why not?" asked Emily. Pete sighed. The Doctors could tell that he knew what news was coming.

"I'm sorry, Pete. I'm sorry, Johnny and Emily Apple," said the Present Doctor. "I'm so, so sorry but...the three of you have to die."

The Abyss

Chapter 6: The Abyss

Sweet Apple Acres/St. Markus Church, Ponyville/London, Equestria/England, Gaia/Earth, Summer/Autumn, 996 C.E./1987 A.D.

Pete sighed and looked at Rose sadly. He wasn't surprised...but that still didn't make him feel any less worse about the situation. Johnny held Emily close. They didn't want it to be true...but it was.

"So...the only way for everything to return to normal...is if we die?" Emily asked.

"Yes," the Present Doctor replied sadly. Applejack turned to her parents.

"Ah...I'm so sorry about all of this," she said. Emily took Applejack and held her close.

"Don't be sorry, Applejack. You did what you felt was right. I'm glad I was able to see what my Applejack would grow up to become. It's apparent that she's going to grow up into quite an amazing mare."

"Ah love you, Mom. Ah love you, Dad."

Johnny walked over and hugged Applejack too. Rose turned to her father and hugged him.

She looked up at him and said, "I-"

Pete stopped her.

"You don't have to say anything, Rose. It's all said and done," he said. Rose stepped away from her father. Johnny and Emily let go of Applejack and then turned to go say goodbye to the younger Applejack, Big Mac, and Apple Bloom.

"What's going to happen when everything returns to normal?" Derpy asked.

"Everyone and everypony else will forget that any of this happened," the Present Doctor replied. He looked past Rose and his past self just in time to see a shady vision of Rose and the Past Doctor sitting with Pete in one of the church's bleachers. The vision faded soon afterwards. The Doctor looked at Rose and his past self and said, "And you'll forget this too."

"What?" Rose asked. "Why?"

"This was never meant to happen: the collision of our two paradoxes. Something else was meant to happen instead," the Past Doctor replied.

"Correct. I knew there was a reason why I don't remember any of this. Once everything returns to normal, you two and everybody else from the church will return to the moment right before our paradoxes collided. This meeting will have never happened," said the Present Doctor.

"So, when I touch my past self, we won't end up here. Future Doctor, what's going to happen?" Rose asked.

"I think it's clear that you and me are going to make it out alive, and so will everybody else. That's what matters."

The Doctor turned and began walking away. At the last second, he turned back and said, "Rose Tyler, it was a pleasure seeing you again. I...I'm going to continue missing you. I will always miss you...as I will continue to miss everybody else."

He then turned away and walked towards the barn/church doors. Rose was silent. She looked up at her own Doctor but couldn't find any words to say.

"Don't think about the future, Rose," said the Past Doctor. "Let's just try to focus on the present...until we get out of here."

Rose finally managed to say, "But...what he said-"

"Doesn't matter to us anymore. We'll forget all about it once everything is set right."

"I guess you're right."

Johnny and Emily approached the Present Doctor. Pete was standing next to them. The younger Applejack and Big Mac were comforting each other and Apple Bloom in the corner of the barn.

"You're ready?" the Doctor asked.

"Yes," replied Johnny, Emily, and Pete with nearly stone-cold expressions. They had no more sadness left to show. The stage of grief had past. It was time for them to set things right.

"How...how are we going to do it?" Johnny choked. The Doctor thought back to how Pete had originally sacrificed himself the first time. The car that had run him over had kept coming back to finish the job. But, this time, there was no car. There was nothing outside the church except a black oblivion and a burning ball of fire. Then it hit him. The ball of fire.

"I think I know how," he replied with a tinge of grief. Suddenly, the entire building shook around them. Holes and cracks began appearing in the walls, floor, and ceiling. Some were normal cracks but others looked out of this world. They emanated a white light that was too bright to look at. The Reapers cried again as they began clawing their way into the barn/church.

"What's happening?!" Rarity shrieked. The building began falling apart all around them.

"This is it! The final merging!" the Past Doctor stated in shock. The floor disintegrated beneath them and everybody and everypony fell down into the dark abyss beneath them.

The army of Reapers went crazy. They scooped up some of the falling humans and ponies and proceeded to devour them. The Present Doctor expected to see the ball of fire beneath him but instead saw bits and pieces of different times and places floating in the abyss. The clock from the London Clock Tower flew by him. He managed to grab onto a chunk of the roof of the Sweet Apple Acres farmhouse. Spike landed next to him. Derpy, Rainbow Dash, Fluttershy, and the pegasi known as Sarah were able to stop themselves from falling by flying but the Reapers quickly turned on them.

"Rainbow Dash! Derpy! Fluttershy!" Spike cried. The pegasi tried to escape but the Reapers were too fast. The Doctor watched as more of his friends became meals for the hungry beasts. Twilight landed on a piece of Georgian Road alongside the Past Doctor, Rose, and Pete. Applejack, Johnny, Emily, and the young Mickey Smith had landed on top of a piece of the St. Markus Church roof that was floating a few feet away.

"Duck!" cried the Past Doctor. Two Reapers flew down and snatched up Twilight and Pete.

"No!" Rose cried.

"Twilight!" Spike screamed from above. Applejack was in shock. Was this the end? Would this be the end? Johnny and Emily held onto each other. Mickey began falling off the roof. Applejack rolled over and grabbed onto him.

"Gotcha!" she said. The Reaper that had devoured Twilight turned back and began flying towards Applejack and Mickey. Johnny and Emily looked over the edge. That's when they saw it. Floating far beneath them was a burning grain silo. Fire lapped its sides and plumes of smoke seemed to reach up towards them like the arms of a hungry monster. The two ponies looked at each other and then towards Applejack.

"Will it work?" Emily asked.

"There's only one way to find out," Johnny replied as he kissed her.

"For our children."

"For the world."

Applejack turned back just in time to see her parents jump off the edge of the roof, still holding onto each other. She looked just in time to see the Reaper flying towards her.

"Goodbye, Mom. Goodbye, Dad," she said as she closed her eyes and let the Reaper consume her.

The Past Doctor and Spike looked down and watched as Johnny and Emily plummeted towards the burning grain silo.

"This is it," said the Doctor. "Time will either fix itself or we'll be doomed to perish in this dark void."

The Past Doctor held tightly onto Rose.

"Whatever happens, don't let go," he told her.

"Don't worry, I won't," she said back to him. Johnny and Emily looked down. The grain silo was coming up fast. Emily closed her eyes and tightened her grip around her husband. Johnny closed his eyes too and gave his wife one last kiss on the cheek. They didn't feel anything when the fire wrapped around them and removed the life from their bodies.

The Present Doctor and Spike looked as a bright, white light began expanding through the abyss. The Reapers screamed and tried their best to fly away from the light, though it was to no avail. The Past Doctor and Rose held onto each other as the light wrapped around them. The Present Doctor and Spike watched as the light engulfed them. The Doctor closed his eyes. He could feel the clocks going backwards and the cracks mending around them.

"Goodbye, Rose," he whispered to himself before he lost consciousness.

St. Markus Church, London, England, Earth, Autumn, 1987 A.D.

Rose was in tears as she handed the vase to her father. Was this really the only way to fix what she had done? Yes, it was. This truth pained her. She had been so close to having her father forever. If only she hadn't touched her infant self. If only the Reaper hadn't appeared and had devoured the Doctor. That's what this event would be remembered as. It would be just one, giant if only.

"Are you going to be there for me?" Pete asked as Rose handed him the vase. Rose choked through her tears to answer her father.

"Yes! I will!" she cried. Pete placed his hands on Rose's shoulders.

"Thanks for saving me."

Rose then hugged her father for one last time.

The Reapers were still flying around the exterior of the church. Pete, with the vase in hand, ran out and looked up as one Reaper began flying towards him. He turned towards the end of the street to see that familiar, tan car appear out of a golden rip in time and space. He broke into a run. The car was coming up fast. He ran straight into the middle of the intersection. The driver threw out his hand and the car swerved violently.

"Goodbye, love!" said Pete as he closed his eyes and prepared for the impact. The car smashed into his body and the vase fell to the ground with a loud crash.

Rose stood in front of the church. All of the Reapers disappeared in a flash of golden light. She watched as her father lay in the middle of the road. She felt a hand on her shoulder. It was the Doctor.

"Go to him. Quick!" he said. Rose took off towards her dying father. The driver of the tan car stood there in shock. Rose knelt down next to Pete and held his hand tightly. Pete gave a small smile before dying in his daughter's arms. As the now alive and well wedding party began coming out of the church to inspect the scene, Rose stood up and silently followed the Doctor back to the TARDIS.

The Girl Who Stayed

Chapter 7: The Girl Who Stayed

Sweet Apple Acres, Ponyville, Equestria, Gaia, Summer, 996 C.E.

The Doctor opened his eyes. He was standing on top of the hill where the TARDIS had originally arrived at. He looked and saw that everypony else was there with him: alive and well.

"Trixie!" exclaimed Pinkie Pie and Fluttershy. The cloaked unicorn rubbed her temple as the two mares hugged her.

"What just happened?" she asked. "One minute that thing was flying at me and the next minute I was standing on this hill again."

"A time monster ate you but you're okay now!" Pinkie said with a smile.

"Oh."

Spike ran to Twilight and hugged her. She hugged him back.

"I swear, Twilight, you're starting to develop a habit of giving me heart attacks!" he snapped.

"I know and I apologize. I think some R&R will help put a stop to that," she replied.

"Some R&R sounds pretty good right now!" Rainbow Dash exclaimed. "Right, AJ?"

Everypony fell silent. Applejack was staring off towards the farm. A large storm cloud and a tower of smoke could be seen rising into the sky. Applejack took in a deep breath and exhaled silently.

"Applejack?" Rarity asked. Applejack let out a small chuckle.

"Hey, Doctor?" she asked. "Do you remember how ah told you how nopony ran to save my parents when the grain silo caught fire?"

"Yes," he replied with a curious tone.

"Well, ah think that particular detail just changed."

"What do you mean by that?" asked Derpy as she stretched her wings.

"Big Mac was holding me down, preventing me from running into the grain silo. Ah was screaming for my parents and that's when ah saw them. Two ponies, running straight for the grain silo. Ah couldn't make out who they were but ah could tell that one of them was a mare and one of them was a stallion. Both of them ran into the grain silo...but they never came out. After the fire, my parents' bodies were discovered but that other mare and stallion were never found. Ah always wondered what happened to them. Who they were. Why they ran to save my parents. If they survived or perished in the fire along with them. Ah think I just got my answer."

The Doctor walked up to Applejack and placed a hoof on her shoulder.

"Are you going to be all right?" he asked. Applejack looked out towards the burning grain silo in the distance.

"Ah don't feel so good right now, but ah will feel better in the future. Ah got to see my parents again. That's all ah really wanted to begin with."

She then gave a small smile and followed it with a chuckle.

"Come on, everypony," said Twilight. "I think it's time that we went home."

"Right!" said the Doctor. "So, Trixie, where would you like to be dropped off?"

"Canterlot in 1002 would be nice," she replied with a smirk.

"Canterlot it is!"

The Doctor and Trixie were the first to enter the TARDIS. The others followed suit. Applejack was still a bit down but Rainbow Dash placed a wing over her to help cheer her up a bit. Twilight and Derpy found themselves outside by themselves for a moment.

"Well, we better get going," said Twilight.

"Yeah," said Derpy. She looked at Twilight awkwardly. "I guess we're not the first ones to have feelings for the Doctor."

"I guess not."

"I wonder what happened between Rose and the Doctor. Has the Doctor ever mentioned to you about why he stopped traveling with her?"

"Yes, though he didn't tell me all of the details. He just said that some things happened and she ended up trapped in an alternate universe."

"How sad. I wonder why he hasn't gone to see her yet."

"Well the TARDIS couldn't travel through dimensions so it was practically impossible for him to ever see her again."

"But it can now. Do you think we might run into her again?"

"It's possible, I guess."

"What will happen then?"

"I don't think you or I have everything to worry about. The Doctor told me that Rose has a Doctor of her own now."

"She has her own Doctor?! Lucky!"

"We better go in before the Doctor leaves us."

"Right."

The two mares smiled and giggled as they walked into the TARDIS. The TARDIS then slowly dematerialized as the grain silo continued to burn in the distance.

Powell Estate, London, England, Earth, Autumn, 1992 A.D.

The six-year-old Rose sat next to her mother on the bed as a photo album was presented to her. A picture of her father, Pete Tyler, stared back at her. She listened as her mother talked about the day he died. She talked about him being late to the wedding and running out into the street where he was hit by an oncoming car.

"The driver was just a kid. He stopped and waited for the police. It wasn't his fault. For some reason, Pete just ran out," said Jackie. "People say there was this girl, and she sat with Pete while he was dying. She held his hand, and then she was gone. Never found out who she was."

"Where do you think she is today, Mummy?" Rose asked.

"I don't know, sweetheart. But I hope she went on to have a wonderful life. I really do."

To be continued...