Chapter 1: Blueberries
Canterlot Castle, Canterlot, Equestria, Gaia, Winter, 1002 C.E.
Twi's ears were ringing. That's all she could hear clearly: a constant, annoying ring. Every other sound around her was dulled to the point of sounding like their sources were on the other side of the city. Dust flew about the air and several projectiles ranging from gun blasts to magic spells raced past her head.
The converted Celestia, now known as Black Sun, unloaded a sea of magical blasts and ammo down upon everyone and everypony in the room. Celestia the alicorn cast a huge protective shield between them and Black Sun but it was obvious that it wouldn't hold the attacker back for very long. "We can't let her get to the Elements!" the Princess stated.
"We're only going to be able to hold her back for so long," said Twi. She and Celestia faced each other. "Princess, the Elements can't stay where they are. Eventually, Black Sun is going to get through all of us and anything else that stands in her way."
Celestia sighed and nodded. "You're right. We must get the Elements away from here and get them somewhere safe."
"But where?!" asked Luna the alicorn. "What place could be safer than here?"
Celestia thought for a moment. "I know a place," she eventually responded. "The TARDIS. The Doctor's TARDIS. Right now, there's no safer place in Equestria."
"But the TARDIS is inaccessible right now, Sister! Remember? The Doctor said that he put it a second out of sync or something like that."
"Then we need to fetch the Doctor from the Crystal Caverns."
"Leave that to us," said Twi as nodded her head at Flash and Shining Armor.
"Be careful," said Celestia. "It's a maze down there."
"We'll find him, Princess." Everyone jumped as Black Sun punched the shield, causing it to crack. "And we'll be quick about it too."
"Sister," said Luna the alicorn. "Go protect the Elements until the Doctor returns. I will hold off Black Sun for as long as I can."
"Correction," said Luna the human, who had been standing silently off to the side for quite some time. "We will hold her off." Celestia and Alicorn Luna shared a nervous glance. "I also have help on the way. Black Sun isn't going to get anywhere near your Elements of Harmony." Both Lunas looked ahead and prepared themselves for the continued fight with Black Sun.
Celestia looked at Twi for one last time. "Again, be careful," she said.
"You too, Princess," Twi said back. Celestia gave a small smile before spreading her wings and flying off in the direction of the Elements. Meanwhile, Twi, Flash, and Shining Armor dashed for the entrance to the Crystal Caverns.
Luna the human let a single tear fall as she readied her weapons. She lunged into action as soon as the shield was broken.
Zecora's Hut, Everfree Forest, Equestria, Gaia, Winter, 1002 C.E.
Oswin awoke to a pain in her side and the sounds of frightening cries and howls reverberating around her. Upon sitting up, she saw that she was on a cot within a dimly lit room. Through the darkened light, she could make out the unconscious figures of Monty and Francis lying on two separate cots.
"Keep it up, Trixie!" cheered the voice of Julianna from below.
Oswin clasped her forehead as she stood up and limped her way towards the nearby stairwell. She grabbed the wall to keep herself balanced while she cautiously walked down the steps. Each step she took felt like it was draining a little spark of energy from her. She knew that she probably needed more rest but she had to know where she was and what was happening first.
Trixie breathed deeply as she focused on the task at hand. She could feel sparks bouncing all across her body and her horn was tingling something fierce. Julianna's encouragement was slightly helpful but she knew the just simple cheers wouldn't be enough to keep her focused for that much longer. She breathed slowly and tried to clear her mind as much as possible. All she wanted to do was focus on the task at hand: keeping whatever was outside from getting inside.
"It is working! You are driving them back!" said Zecora with a smile. "Make sure your focus does not crack!"
Already making sure of that, thank you very much, thought Trixie as she continued to focus on keeping the magical shield around Zecora's hut stable. She could feel the creatures outside smashing and pounding the exterior of her shield. She cringed with every blow and shook with every crack. She wouldn't be able to hold them back for long, whatever they were. They needed to find some way out of there. Some way to safety.
"What...what's happening?" groaned a tired voice. Trixie glanced back to see a weary Oswin leaning against the side of the threshold to the upper level of the hut.
"Oswin!" gasped Julianna as she raced to the human's aid. Oswin stumbled forward and knelt down on the floor. It was obvious that she was still getting over her injuries from the crash. "Are my dad and brother awake yet?"
Oswin shook her head. "No. Just me. What's going on? What are all those noises?"
"Creatures from the dark, I fear," replied Zecora. "We most certainly don't want them in here."
"Well it won't be long before that happens," groaned Trixie. "I'm not sure I can hold them back that much longer."
"There's got to be some way out of here!" said Julianna as she turned to Zecora. "Do you have some sort of secret passageway or something?"
Zecora shook her head. "I never had any need of that, you see," Zecora said. "I'm afraid there's no way out of this tree."
"Aw come on!" Julianna turned her attention to Trixie. "Why can't you just teleport us out of here?!"
"I'm not skilled enough to perform teleportation spells yet!" Trixie replied with a look of shame on her face. "Though I wish I were."
Zecora's face suddenly lit up. "I just remembered a special brew! It may indeed aid you with what you wish to do!" The zebra raced over to one of her cabinets and began searching through an array of bottled liquids and ingredients. The light on Trixie's horn was starting to flicker. With each flicker of the horn, the sounds outside seemed to grow louder and more aggressive. Suddenly, Zecora emerged from her cabinet with a vial of purple liquid in her hooves. She raced over to Trixie and presented the vial to her. "Drink this, unicorn, and focus still. It should help you enhance your skill." Without hesitation, Trixie opened her mouth and allowed Zecora to feed her the unknown solution.
As soon as the final drop of liquid slid across Trixie's tongue, a powerful blast of energy surged through her body. Every part of her body grew incredibly hot and her eyes emanated a harsh, blue light. Powerful waves of energy emanated from her horn and coursed through the air. Zecora, Julianna, and Oswin were taken by surprise as the waves of magical energy hit them and threw them across the floor of the hut. The howls and roars outside turned to cries of terror as the entire hut started to vibrate.
"TRIXIE!" Julianna cried as she and Oswin held onto each other.
Trixie could feel tears rolling down her face as she tried her best to focus on the task at hoof without allowing the energy inside her body to take control. She thought about safety: saving herself and those around her. She thought of past regrets, remorse, familiar faces. She knew where she wanted to be right now. She knew who she needed to see. A loud scream echoed from deep inside her as a blast of magic erupted from her horn and engulfed the entirety of Zecora's hut.
Oswin put a hand in front of her face as Trixie became a glowing ball of energy. The cries of the creatures outside seemed to fade away and be replaced by that of the roar of a passing train. The hut started to spin...or were just those inside the hut spinning? Oswin was unsure of what was happening. She felt as if a powerful, yet loving, hand had wrapping itself around her entire body and was now taking her somewhere else. The light soon became so bright that she was forced to close her eyes. Eventually, she stopped resisting and allowed the raw magic to overtake her senses. Everything faded away into a long, angry roar.
Ponyville Hospital, Ponyville, Equestria, Gaia, Winter, 1002 C.E.
Daring Do was angry. All she could think about was being taken down so easily while her allies had been stolen away with next to no resistance. Where were they now and were they even alive? What had that sadistic human Pinkie Pie done to them by this point? Daring didn't have any answers and it absolutely infuriated her as much as it did worry her. She was stuck in a state of painful limbo now, held at the mercy of a vicious knife wound. Concerned, professional voices echoed around her but she wasn't able to understand what they were saying.
Then, without warning, the talking stopped and was replaced with gasps. A muffled boom met Daring's eardrums. She could feel vibrations reverberate through both her body and the air around her. A spark of strength seemed to follow the vibrations as she almost instantaneously sat up and opened her eyes.
Though her vision was mostly blurry, she was able to determine where she was: in a hospital room. The sharp scent of sanitizer attacked her nostrils like snakes and a cocoon of bandages surrounded her torso. In the mostly white room, she was quickly able to notice the bright blue light shining through the nearby window.
"Well then," she groaned. "What do we have here?" She was able to give a curious grin before losing her ounce of strength and falling back down onto the hospital bed.
Discord Laboratory, Beneath Rainbow Falls, Equestria, Gaia, Winter, 1002 C.E.
Thalia could smell blueberries. Did she like blueberries? Did her original like blueberries? Should she like blueberries? Did she even want blueberries?
"Hey! Wanna muffin?" asked a cheery voice. Thalia opened her eyes. She was lying on a bed in an overly pink bedroom. She couldn't remember how long she had been there. How long had she been asleep? Had she even fallen asleep in the first place? She looked to her left to see the odd creature with pink hair staring her down. A plate of blueberry muffins was clutched in her hands. "Try one! They're really good! They could have used a couple ounces of pegasus, if you ask me, but Mr. Whooves thinks you're better off staying away from cannibalism right now." The young woman placed the tray on a table standing next to the bed. Thalia slowly sat up, reached for the tray, and grabbed one of the muffins. Once in her hoof, she examined the edible object carefully. Everything about it fascinated her. Its warm, soft exterior. Its wonderful aroma. Its nonverbal calling of it to be consumed. "Are you going to eat it or stare at it? It's fine either way. I stare at my food sometimes too. Mostly before it's been killed but to each their own."
Thalia glanced at her strange visitor. A part of her brain was repulsed by the words she was hearing. Talk of cannibalism and killing. These were bad things, Thalia was sure. Or, at the very least, a part of her was sure of this. She turned away from the woman with pink hair and focused on the muffin once again. She could decide whether or not she despised the woman later. Right now, she had something to eat.
She brought the muffin to her mouth and bit down. Instantly, she was met with waves of pleasure emanating from her tongue. The taste was amazing. Now all she could think about was the taste of the blueberry muffin. Who was she repulsed by? She couldn't remember. All she could focus on was the wondrous item being broken down within her mouth.
A shrill, annoying laugh broke her concentration. She turned to see the strange woman laughing at her. The muffin was no longer in her mouth now. It had passed on to the next stage of digestion, leaving remnants of its taste clinging to parts of Thalia's mouth. Her glorious distraction was gone. She had to focus on the woman again. This was something she wasn't particularly looking forward to.
"You looked so funny when you ate that!" giggled the woman.
Thalia blushed and slid away from the woman. "I...I wasn't trying to be funny," she said softly.
"Oh! You're talking now! Mr. Whooves is going to love this! I better go get him!" The woman turned around and skipped out of the room.
Thalia wasn't keen on waiting for the woman to return. She cautiously got up from the bed and made her way across the room to the door the woman had passed through. Thalia sighed with relief as she pushed the surprisingly unlocked door open. Instantly, she was met with a foul scent. It was familiar. She remembered smelling it when she had woken up for the very first time.
Beyond the door was a long hallway with metallic floors and brick walls. Everything was grim and gray and dim lights on the walls cast horrible shadows. At first, Thalia was nervous; but she hastily took a deep breath and calmed down. With caution, she chose to turn left and proceeded down the hallway.
It wasn't long until she reached the first hallway intersection. The hallway she was in ended in what appeared to be the middle of another hallway. Her ears twitched as she heard the sound of muffled voices echoing through the air. She was relieved that none of them sounded to be coming from the weird woman who had brought her muffins. She wanted to talk to somepony. Anypony. Well, anypony aside from the weird woman. She was still pretty unsure about her.
Thalia turned right and followed the voices to a pair of metal doors located a little ways down from the intersection. She pressed her ears against the doors and listened.
"They've been gone for a while now," said one female voice.
The sounds of moving chains and stretching leather could be heard. "Rainbow Dash, don't tire yourself out. I don't think pulling and struggling is going to get us out of here," sighed another female voice.
"There's got to be a way out of here!" snapped a voice presumably coming from the one known as Rainbow Dash. "I'm not going to just wait around and see what they're going to do to us!"
Thalia noticed the sound of flames being blown. "Any luck, Spike?" asked another female voice.
"No," replied the one known as Spike. "He must have made this cage fireproof or something."
A deep sigh could be heard. "Considering what he's already done with me, I think I have an idea of what he has in mind," said an incredibly familiar voice.
"You mean...he's going to make clones out of the rest of us?" asked a shy voice.
"I wouldn't doubt it."
"But I don't understand," said the elegant one. "Why make clones of us?"
Thalia didn't notice that the doors were slowly opening inwards. She let out a gasp as the doors flew open and she fell forward onto the floor. She rubbed her muzzle and looked up to see a circular room occupied by a group of mares chained to slanted medical tables. She could also see a cage holding a pegasus mare and a little dragon. A sharp pain rushed through her head as her eyes fell on all of them. She knew that she knew who they were and yet she couldn't recall a single thing about them.
"What are you doing here?!" snapped the cyan pegasus who Thalia identified as Rainbow Dash. "Well?!"
Thalia jumped up and nervously shuffled her forelegs. She looked to see that everypony in the room was glaring at her. All except one: Twilight Sparkle.
"Twilight...Sparkle," she said as her gaze fell upon the lavender unicorn, who was staring at her not with hatred but with fear and uncertainty. "Why...are you looking at me like that?"
"Because you're a meanie, that's why!" snapped the pink mare.
Thalia gave a confused look. "A...meanie? Have I done something bad?"
"You bet your rump you have!" Rainbow Dash snarled.
"I'm...sorry. I don't remember what I have done."
"It's not what you've done," sighed Twilight.
Thalia cocked her head. "Well...what have all of you done?" she asked.
"Pardon?" asked the orange mare with a raised eyebrow.
"You must have done something bad to end up in a room like this."
"I do believe you've got things mixed around," stated the white mare.
"Mixed...around?" Thalia asked.
"Ah! There you are, Thalia!" laughed a voice from behind. Thalia turned around and smiled. Standing before her was the stallion who had named her. The stallion who had been there when she woke up. The stallion who...looked rather dashing. "Pinkie was telling me that you've started talking! Is that true?"
"Uh...yes. It appears...so," Thalia replied with a blush.
"Excellent! You're developing quite nicely, my little mare!"
"Thank you. Mr. Whooves, is it?"
"You can call me that. Or you can call me Discord Whooves or Mister or even Discord. But never call me Dr. Whooves."
"Why not, Mr. Whooves?"
"Because I'm not a Doctor. I am so much more."
"That's debatable," snarled Twilight.
"Believe whatever you want to believe, Twilight Sparkle," chuckled Mr. Whooves. "But the truth of the matter is that I will be victorious." The gray stallion entered the room and approached Twilight. "Who do you see before you now, hmm? Certainly not your Doctor. No. You see me: Discord Whooves. Your Doctor is out there somewhere running about. He's probably forgotten you by this point."
"That's a lie, Discord Whooves. If there's anything I know about the Doctor, it's that he never forgets his friends."
"Is that so? Believe me, Ms. Sparkle. There have been plenty of others before you. Others who have left him. Others whom he has left. Others who have been lost. I'm sure you already know this. It appears you already know Donna Noble." Twilight remained silent. Thalia continued to watch Mr. Whooves with awe. "But there's been many, many more." His eyes twitched slightly as he leaned in closer to Twilight. "Susan, Barbara, Ian, Jamie, Zoe, Jo, Sarah Jane, Adric, Tegan, Peri, Ace, Rose, Martha, Donna, AMY!"
Both Thalia and Twilight jumped a bit. "So who's Amy?" asked Rainbow Dash with a snide look. "I don't recall our Doctor mentioning her but she seems to be special to you."
"Who's Amy, you ask?" Mr. Whooves slowly turned and walked over to Rainbow Dash; and, in the blink of an eye, he raised a hoof and slapped her across the face.
"HEY!" snarled the orange mare. "DON'T YOU DARE TOUCH HER!"
Mr. Whooves laughed as he slapped Rainbow Dash again. He then raced over to orange mare and laughed in her face. "I'll touch her as much as I please, Applejack! As long as you're in here, you're my property!" He then stroked Applejack's face with his hoof before calmly turning back to Rainbow Dash, who was glaring at him with daggers in her eyes. "To answer your question, Rainbow Dash, Amy was a girl who waited for a madman. In the end...it wasn't worth it." He fell silent for a few seconds before turning to Thalia with a wide grin. "Come along, beautiful. We've got work to do."
Thalia blushed again as Mr. Whooves wrapped a foreleg around her and began leading her out of the room. Before the doors closed behind her, Thalia looked back and shared one last stare with Twilight Sparkle: her original. She looked into the other lavender mare's eyes and saw many things: sadness, fear, pain, anger. But there was one thing she saw that appeared to overtake everything else within her original. Something so powerful it seemed to make Twilight's eyes sparkle: hope.
The doors slammed shut and Thalia looked up at Mr. Whooves as he led her down the hallway. "Before we get to work," he said. "Would you like anything, my dear?"
Thalia giggled. Despite the stallion's insane and extreme nature, there was something about him that drove Thalia wild. Her cheeks turned bright red once again as she looked up at the stallion and nodded. "Blueberry muffins would be nice."
Mr. Whooves chuckled and pulled Thalia in closer. "Blueberry muffins it is."