//------------------------------//
// A Flaw in the Plan 
// Story: Doctor Whooves Episode 2: The Awakening 
// by Doctor Perseus 
//------------------------------//


Chapter 4: A Flaw in the Plan


Old Barnaby Station, Underneath Ponyville Central, Equestria, Gaia, Spring, 2002 C.E.

The Doctor, Charlie, and Juliet fought their way through another wall of cobwebs and found themselves standing on the platform of an old subway station. The station was built into the side of an underground chamber and the chamber was large enough to hold three train yards. Several different old train tracks were laid out throughout the chamber but the only one that led out of there was a single track that ran alongside the platform.
"This station used to be used constantly but it got shut down after the depression of the 1640's," said Juliet. "The cars were specifically made to be moved by either unicorns or alicorns. And, luckily, there happens to be a car right here."
The train car that Juliet pointed to resembled that of a trolley that the Doctor had seen riding through San Francisco.
"Truly marvelous! I'm still impressed by how much you lot have advanced in just this short amount of time!" exclaimed the Doctor. They then entered the trolley and Juliet walked up to the front. 
"Now, according to what I've read, these trains can go really fast so we should be in Canterlot in at least half an hour."
"Then let's go! Allons-y!"
Juliet nodded and her horn began to glow. The train car slowly moved forward and soon they were racing down the track. The Doctor and Charlie sat down across from each other to wait out the ride.
"So what were two doing down here, again?" asked the Doctor.
"Juliet's mother sent us to go down and look for you and Twilight with Crisp Oaks, the head of Sweet Apple Industries," Charlie replied.
"How did they know that we'd be in this time period at all?"
"There are countless stories about you and Twilight Sparkle."
"There are?"
"Yeah. Now, granted, some of the facts have been warped and a majority of the stories are works of fiction, according to the Headmistress, but they're still classic stories."
"If they're so classic then how come you two don't know Thalia or about what's supposed to happen?"
"It's funny. I've read a fair amount of your stories and I have a friend who's completely crazy about you. He's told me about every story and none of them talk about you arriving in this time period."
"Then how could your Headmistress or this Crisp Oaks pony know anything about it?"
"I'm still trying to figure that part out."
"We should be there shortly!" Juliet called. The Doctor and Charlie turned back to each other, laid back in their seats, and waited.

Chariot Pass, Outskirts of Canterlot, Equestria, Gaia, Spring, 2002 C.E.

The Headmistress and Queen Luna stared out upon the grand city of Canterlot. Queen Celestia was no doubt sleeping peacefully in her bedroom. The TARDIS would be close by her. 
"You ready, Sarah?" Queen Luna asked. "Are you ready to fulfill history?"
Sarah Sparkle looked down at a large bag hanging around her back and she nodded. 
"I've read the story countless times. I know how it's all going to play out," she replied.
"I still don't understand why you've never let anypony else read the story. You've only told your secretary, Crisp, and myself. You haven't even told your daughter about it."
"Like the Doctor said, or says, "Some points in time are fixed and some are in flux." This is a time that's definitely fixed. I have to let it play out like Twilight Sparkle wrote it out. Otherwise time itself would unravel and we'd be caught in a never-ending paradox."
"You've put a lot of thought into this, haven't you?"
"I've read that story hundreds of times since I first read it as a young foal. I read all the stories and have spent years of my life dedicated to studying the history of Equestria, and most notably that of the Doctor and my ancestor. Of course I've put a lot of thought into this."
"Then, if you're ready, let's head down there and finish something that should have been finished years ago."
"I couldn't agree more."
With that, Luna used her magic to open up a small cave entrance that stood on the side of the train tracks leading into Canterlot. Sarah was the first to enter and Luna followed suit, making sure to close the entrance as she entered.

Crystal Station, Underneath Canterlot, Equestria, Gaia, Spring, 2002 C.E.

The train car came to a halt and the trio of heroes hopped out. This station wasn't as big as the one they had previously been in but it was definitely in better shape. The walls were made of solid marble and granite and chunks of glass and crystals shone from the walls. The Doctor wanted to stay and admire the architecture but this was not the time to do so. He had a friend to save. 
"So what is this place?" asked the Doctor.
"This place is known as the Crystal Caverns. They used to be used as a dungeon for war criminals in the early years of Equestria. In fact, the spot where Canterlot sits now used to be a massive prison. They were forgotten following the fall of King Discord to the Queens and weren't rediscovered until 1002. It wasn't until 1291 that the Queens decided to start using it as an underground transportation system. But, like I said earlier, the depression of the 1640's caused it to become abandoned again," said Juliet.
"Seems like the perfect place to hide."
"Yeah. It sure gives me the creeps," Charlie croaked. They walked through the interior of the station until they came across a blocked stairwell. "I'm guessing that leads up to the city."
"Used to. There has to be another way out of this station and into the main caverns," said Juliet. They began examining the area and the Doctor pulled out his Sonic Screwdriver. Using it with his mouth was definitely strange but it's something that he was getting used to pretty quickly. He aimed it at a nearby wall of glass and activated it. The light hit the wall and it shook a bit. The wall slid aside to reveal a long and incredibly dark passage.
"This Thalia sure likes to use secret passages," the Doctor chuckled.
"It's pitch black in there!" said Charlie. "We wouldn't be able to see our hooves in front of our faces!"
"I can take care of this," Juliet said. Her horn then began to emit a dim bluish light. "It's not the best illumination spell but at least we won't be blind."
"Perfect!" said the Doctor. "Onwards!"
Charlie gulped as they entered the dark passage.
There wasn't much room inside the passage. In fact, it was only wide enough for two ponies to walk next to each other with a little bit of space between them. Juliet took the lead while the Doctor and Charlie walked behind her. 
"You okay?" the Doctor asked Charlie.
"Fine. Could be better though," Charlie responded.
"I take it that you're not fond of being underground."
"I'm not fond of a lot of things."
"Then why did you agree to come and help Twilight and I?"
"The Headmistress kind of sent me. I didn't have much of a choice."
"But you didn't protest."
"How do you know that I didn't protest?"
"The way you're acting. Sure you're unsure, frightened, and somewhat nauseous but you're not constantly complaining or running away from danger. That proves that, somewhere in your mind, you want to be down here."
"I don't know."
"Think about it."
Charlie nodded and looked forward again. The tunnel slowly began to widen out until they came to a large, open room. The Doctor pulled Charlie and Juliet back as an explosion of light began emitting from the room.
"Stay back and keep quiet!" he whispered to the two ponies. "And, Juliet, turn off your horn!"
The light around Juliet's horn faded away and they turned towards the room. The Doctor crept in front of Charlie and Juliet and looked around the corner. 
Twilight was there but she was strapped down. There was a pair of cloaked Applejack clones laying unconscious in the corner of the room. In the middle of the room there was a mare. A mare with a pale white coal, night black hair and eyes, and a look very similar to Twilight. It was then that the Doctor realized that this mare was a Twilight clone! The clone laughed and approached Twilight. She then proceeded to gloat in front of Twilight and mock her. 
"Enjoy these last few breathes of air, Twilight, because soon you won't have to worry about breathing anymore," she chuckled. The mare walked over to a nearby table and grasped a butcher's knife in her mouth. Twilight struggled at the bonds but she couldn't break free. "This...will be fun."
The Doctor couldn't wait any longer. He stepped out from behind the corner and casually walked over to the spot where a tub of water once stood.
"You know, you should really redecorate this place," he said. The Twilight clone, who had revealed herself to be infamous Thalia, turned around. The knife fell out of her mouth and hit the floor.
"How the hell did you escape my animals?!" she asked.
"I had some help."
Charlie and Juliet emerged from the shadows and stood behind the Doctor. 
"How charming. You've formed your own rescue team!" Thalia teased.
"Yeah well I like teams. Teams make everything fun," said the Doctor.
"Yes. They certainly do. You know, this isn't a hiccup at all. Now I can gain the pleasure of killing both you and her!"
"And you can go along and do that shortly but listen to this. It seems to me you've met us before."
"All too many times, Doctor."
"But Twilight and I have yet to meet you before."
"What do you mean by that?"
Thalia picked up the blade and clasped it between her hooves.
"You see...this is Twilight and I's first real trip together. We haven't met you before. You don't exist yet in our timeline."
"You're lying! You're just trying to buy time."
"That may be but listen. If we've yet to meet you that means you don't exist yet. Now, I'm assuming that you're a clone of Twilight, harvested from her DNA. If you don't exist yet from our standpoint and you kill Twilight now...then how will you end up being created?"
"I...I-"
"Exactly! You wouldn't be created! But then, if you were never created, who would be down here to kill Twilight in the first place? Nopony! Don't you understand?! If you kill Twilight or me...then you prevent yourself from existing altogether! And, in the long run, time would fall apart from the paradox."
Thalia looked down at the ground. She had picked up the wrong Twilight. This was a Doctor and Twilight from before her creation. He was right. She was stuck. But...she didn't care.
"What makes you think that I care by this point?!" she snapped.
"Pardon?" asked the Doctor.
"So what if I destroy my existence?! So what if I cause time to unravel! I'm ready to face that in order to finally feel satisfaction for just a few seconds."
"You're completely mad!"
"And whose fault is that, Doctor?! Who drove me to this point?! You did! You and this lavender bitch! It's time to settle a score."
Thalia turned around and raised the blade. Twilight's eyes widened as the blade came down. 
It all happened in a flash. The blade was a few inches from Twilight's neck when something yellow flew past and smashed into Thalia. The blade flew through the air and embedded itself in the wall. Charlie didn't know what we was doing but he suddenly found himself fighting against a thrashing evil clone of Twilight Sparkle.
"Kill them!" screamed Thalia. The two Applejack clones sat up, their eyes glowing with black energy, and began advancing on the Doctor and Juliet.
"I'll handle these two. You free Twilight!" said Juliet. The Doctor nodded and pulled out his Sonic Screwdriver. It didn't take long for him to undo Twilight's bonds.
"Thank...thank you, Doctor," Twilight breathed. She had definitely lost a lot of blood and she was slowly losing consciousness. 
"Stay with me, Twilight! Stay with me!" pleased the Doctor. Thalia pushed Charlie off of her and threw him into the wall. She then stood up and pointed her face upwards. Her eyes glowed of pure black light. 
"Celestia! The time has come! Destroy the city!" she yelled.

Canterlot Castle, Canterlot, Equestria, Gaia, Spring, 2002 C.E.

The pegasus and unicorn guard in front of Celestia's bedroom had begun talking about a new movie coming out when the bedroom door flew open. Celestia's eyes were completely black and an evil smile was etched onto her face.
"Destroy the city," she cackled. "Destroy the city!"
She flew at the guards, shooting several beams of dark energy at them. They dodged the attacks and fled. The unicorn activated his communicator as he ran.
"Celestia's gone insane! She's crazy! She's trying to kill us! We need backup!" he cried. Celestia then proceeded to begin her unwilling destruction of Canterlot Castle.

The Crystal Caverns, Underneath Canterlot, Equestria, Gaia, Spring, 2002 C.E.

"What? Celestia?" asked a woozy Twilight.
"Yes. It took me some time to expand my telepathic influence while I was still weakened but I managed to drive myself deep into Queen Celestia's psyche," Thalia chuckled. 
"So now, instead of killing us, you're going to have Celestia destroy the entire city above?!" snapped the Doctor.
"Their blood shall be on your hooves, Doctor! You brought this tragedy on those ponies the day you began your campaign against me!"
There was a bright flash and Thalia was gone. 
"Damn! Come on, Twilight!" said the Doctor. Charlie and Juliet were battling the clones but they were incredibly strong.
"How much longer can we hold them off?! Charlie asked.
"Not long!" croaked Juliet. Just then, a nearby wall burst open and a beam of light shot out of the hole. The Applejack clones were caught by the light and they instantly fell apart. Charlie and Juliet turned towards the hole to see that it was none other than Juliet's mother and Queen Luna.
"Mother!" cried Juliet. Sarah had a strange device attached to her hoof that was emitting a lot of steam.
"I knew that you two would be here. How are you?" she asked. Luna looked over and saw the Doctor holding the weak Twilight. Sarah nodded to the Queen and Luna walked over to help.
"Hello again, Doctor," said Luna as she knelt down next to him.
"Princess, I mean Queen Luna? How did you know that we'd be down here?" asked a stunned Doctor.
"Sarah told me. She's known that this would happen for many years."
"How?"
"She's had a story about you and Twilight in her possession for her entire life. Only she has read it."
"Huh."
"What?"
"That was actually for two things. One was for her knowing that this would all happen and the other is the fact that I've just now realized that you and your sister are immortal. My mind has sure been preoccupied with other things."
Luna chuckled and clutched Twilight in her hooves. Her horn began to glow and the wounds on Twilight's body slowly healed.
"Thank...you...Luna," said Twilight as she blacked out.
"So what now?" asked Juliet as she, Sarah, and Charlie approached the Doctor, Twilight, and Luna.
"This device I have is the only thing that can kill Thalia for good," said Sarah as she presented the device on her hoof. "It's a clone destabilizer. It's not a common weapon and it's only used on clones that go rogue."
"Ingenious," said the Doctor.
"Where is she now?" Charlie asked.
"Above in Canterlot. She's probably using Celestia like a puppet now to destroy the city," Sarah replied.
"Luckily the protective spell is down so I can teleport us there," said Luna.
"Then let's go. We need to finish this!" said the Doctor. Everypony nodded. The nods were followed by a bright flash. They were gone.