Chapter One: Covert Operations and realization.

Just outside of Ponyville, in the TARDIS…

"What's so bad about another Time Lord, Doctor?" Derpy Hooves asked. "BECAUSE THEY…. Never mind, I can't explain it right now Derpy. Just trust me; another Time Lord cannot be good for Ponyville, let alone Equestria!" The Doctor exclaimed. The command module gently hummed as the two ponies prepared to go into town. Before they went, however, The Doctor had to check one last time how long Colgate has been known in Ponyville. "The TARDIS found some information on the Time Lord we need to find. Her name is Colgate and apparently she was first spotted in Sweet Apple Acres a few months ago." Derpy recognized the name and told The Doctor "Colgate!? But she is the town dentist! She wouldn't hurt a fly!" The Doctor was shocked that her companion had information on her that the TARDIS couldn't find. "Derpy, how do you know Colgate is the town dentist? I couldn't pull any records on her position of work." Derpy said "Oh, that's easy! She isn't officially our dentist, or at least she didn't have to sign any paperwork. They had an old dentist's building near Sugarcube Corner and since her name was Colgate, the mayor thought she would be good at fixing the townspeople's teeth, though her Cutie Mark is an hourglass…" Derpy was interrupted by The Doctor "Her Cutie Mark is an hourglass!? What type of hourglass? What did the bindings look like?" Derpy continued talking "Well, the rings were gold instead of wooden, like your Cutie Mark and they had strange symbols on them" The Doctor had the same look of shock as before "These symbols, did they look like this watch?" The Doctor pulled a FOB watch out of a part of the console and showed his wall-eyed companion. Derpy studied it for a few minutes, trying to focus her eyes so she could get a more detailed look at the etching on the watch, and then nodded when her eyes confirmed that these were the same etchings seen on Colgate's Cutie Mark. The Doctor suddenly showed a sign of relief "Good. She doesn't realize who she is yet".

Derpy became confused at this remark "Why does it matter if she can't remember that she's a Time Lord?" The Doctor replied "Not all Time Lords are G-." He froze mid-sentence, as if time halted around Derpy. Suddenly a flash of light illuminated and a pony appeared before her. "Who are you?" she asked. "It isn't important right now, but know this: the events about to take shape are the hardest challenges that you and The Doctor will face yet. This is also the same day he reveals what happened to his race to you." The light was beginning to dim around the mare "I don't have much time left! Remember everything I am about to say, as it could save your life as well as The Doctor's. When the moon meets the sun, darkness will spread and a new element will be revealed. Do not tell The Doctor about this conversation. Act like it never happened. I'm sure you have many questions, but the answer to your biggest one is Y-." With that, the light and the mysterious pony vanished and time resumed. "—ood Derpy. Some are evil and I'm afraid it's my fault. Uh, are you okay? You seem... flustered…"

"huh? Oh, yeah I'm fine. Doctor, can ponies freeze time?"

"Not that I'm aware of Derpy. Why do you ask?" said The Doctor.

"Oh, just curious, that's all". With that, the two time-travelling ponies stepped out of the TARDIS and made their way to Ponyville. "Oh, before I forget—." The Doctor pulled out his Sonic Screwdriver, pointed it at the TARDIS and activated it. Soon afterwards, the blue box flashed for a second, then vanished. "Why did you do that?" Derpy asked. "I put it one second out of sync with everything else in the universe. Believe it or not, I have faced an evil Time Lord before. If this one gets a hold of the TARDIS, a lot of bad things can happen to the universe. One more thing: in order to disguise ourselves, I created Chameleon Suits with built in Voice Scramblers that can change our voice and appearance. I would explain how it works, but we are running out of time! We need to know how much the town knows of our mysterious friend…"

Gallifrey, 836 years ago…

"My lord Doctor, thank you for helping me in the exile of Gersillan. I have no doubt you have sensed her connection to you, for I have sensed it too. She will meet you again, somehow; hopefully on better terms than we left her." The President exclaimed "I indeed sense her being tied to my future, but I am not certain as to how far into my future I will meet her again." The President dawned a worried look on his face and thought to himself. 'The Doctor is one of my strongest disciples! If he cannot sense the time period that they will meet again, I fear that it will be soon. I just hope that The Doctor will agree to what I am about to do…' The President spoke again "I am worried that your confrontation with her will be too soon. In order to mask the anxiety from your mind, I would ask you if I could disguise this memory from you in order to keep your thoughts focused…"

The Doctor hesitated for a second, then nodded his head in agreement and kneeled before The President to prepare for his memory wipe. The President put on his Sonic Gauntlet and extended it over The Doctor's head. With a small ringing noise emanating from the gauntlet, The President dived into his mind and masked the memory from The Doctor. He fell unconscious after the memory wipe was performed on his mind. The President called for guards to carry him to a nearby bed and asked them not to disturb The Doctor while he was recovering.

Ponyville, present day…

"Before we go to confront Colgate, we need information! And where can we get information on ponies and their history? THE LIBRARY! Come on Ditzy!" The Doctor exclaimed. As the two made their way to Twilight Sparkle's home, The Doctor decided to test the chameleon suits before arriving. "Derpy put on your chameleon suit. I haven't had time to test them yet, so we might as well now." Derpy did as The Doctor told her and put it on. "Okay, now you see that flashing green and blue button? I want you to press it." Derpy asked: "What does the button do? *gasps* WILL IT TURN ME INVISIBLE!?" she asked with excitement. "No, nothing quite like that. It acts like my psychic paper does, only instead of showing the onlooker whatever document they want to see, it disguises your entire body to whatever pony they want to see! Isn't it brilliant?!" The Doctor exclaimed.
"I guess so…"

When they entered the library, The Doctor told Derpy to play the role of the unicorn Twilight could see as best as she could and if his suspicions are correct, she should see Princess Celestia. As the purple mare came down the stairs, a look of shock and excitement rose upon her face as she looked at Derpy Hooves. "Princess Celestia! It's a surprise to see you here! Why are you with Time Turner?" Twilight Sparkle said. Derpy look confused at this and turned toward The Doctor. He nodded and Derpy spoke. "I know it's sudden, but a matter has arisen in Canterlot and Th-Time Turner is the only one that can help. One of my clocks has broken and since it was made by him, he would understand how to fix it better than other ponies would." The disguised mare said. "Furthermore we came in here to find some books on clocks and how they function. I believe my friend here also wants to get better acquainted with the people of Ponyville and we need a book with all the ponies and how they came into Ponyville." Twilight looked at Derpy for a second with a suspicious glare, but then nodded and handed the books to The Doctor and said "Here you go, Time Turner! If the books haven't given you the information you need, come back again and I'll help you find a copy better suited to you and the Princess's needs." As soon as the two ponies exited the library, The Doctor turned off her Chameleon Suit.

"HA! It worked! This means we will be able to ask questions more discreetly." The Doctor exclaimed. As they were nearing the Dentist's building, The Doctor pulled one of the books out of the saddle bag he borrowed from Derpy. The title read "How to make muffins for foreigners, Vol. 7" Derpy became rose cheeked and swiped the book out of his hand and replaced it with the book he was actually looking for. This book read "A catalogue on the residents of Ponyville, Revised Edition" Looking through the index, The Doctor found the page that had Colgate's information on it. "Ah, here we are!" The Doctor said "According to this, she was found in… no, wait I already knew that. There's the information I was looking for! After Applejack found her in the middle of Sweet Apple Acres, Colgate was sent to the hospital to get checked for any serious brain damage as she was exhibiting signs of amnesia. As soon as she arrived, the nurses saw no damage at all, but curiously enough, Colgate began to help some ponies in Intensive Care that had major tooth problems. According to some of her patient's accounts, she seemed to be an expert on all manner of teeth and knew every weak and strong spot on the—." As The Doctor continued reading, the memories that were suppressed were too much for the barrier The President's Sonic Gauntlet created and snapped, releasing the memories The Doctor had stored away.

The Doctor winced in pain for a moment, and then he realized the full extent that this disguised Time Lord is capable of. "She is alive! This isn't good. No, not good at all! If she ever discovers who she is, this could end up very bad for Ponyville." Derpy asked: "Why is it so bad? You said earlier that Time Lords are sometimes bad, but she couldn't be that bad, could she?" The Doctor turned to his companion with a look of horror, pure horror from what he uncovered from the suppressed memories. "This mare is not just bad, she's insane! If she ever discovers that she is a Time Lord, you and everypony else will be in GRAVE DANGER. Years ago, probably in the early years of your Princesses' rule, I was on my home planet, Gallifrey; before the Time War. I was assigned to deal with an insane Time Lord called Gersillan. My task was to store her memories inside a FOB watch, the same watch I showed you on the TARDIS. When the procedure was complete, Gersillan was cast into the Un-Tempered Schism with her own TARDIS, unaware of who she was or where she was going. She must've landed weeks before I arrived in Ponyville somewhere in Applejack's Farm."

Derpy teared up slightly at this story. "Doctor, what is the Un-Tempered schism? How did she become insane? What was the Time War?" Before Derpy could continue the questions she said, The Doctor answered her. "Something you have to know before I answer any questions, you need to know this: What I did was forced upon me and could always be the only solution I could take." Derpy nodded and The Doctor continued his explanation. "We will start with the Time War. My world, Gallifrey, was always a beautiful world. There were large and numerous mountains with peaks just scratching the surface of the atmosphere, and beyond those mountains lay great meadows of Red Grass, the most beautiful sight anyone could see." Derpy pictured the sight in her mind, becoming in awe at the beauty of his world. "Surrounding the meadows were great forests with silver leaves donned on the trees. When the wind blew through the leaves, they played a serene and beautiful song. In the center of all those was a great city, contained in a glass dome. This was the Citadel where my race once flourished."

The Doctor was beginning to tear up a little. "Then the Time War happened: there were beings called the Daleks who threatened to destroy all of existence. The Time Lords, who at that time were beings of peace, saw what was to happen to all Creation if the Daleks succeeded and went to war with them. The Time War it was called, as the battles were occurring at every point in history. The war waged for 200 years, before the Time Lords came up with a solution. They were going to destroy themselves to ascend into a 'higher form of life, free from time itself'." The Doctor began to sob lightly now as his story was nearing his end. "I had to save them, Derpy. So I locked the entire planet in a Time Lock. Like what I did with my TARDIS earlier, except a whole planet! MY PLANET! I SEALED MY ENTIRE PLANET DERPY! Why couldn't I save them?!"

The Doctor started to sob uncontrollably and the crowd started to stare. Panicking, Derpy escorted The Doctor to a nearby alley to continue his story. "Thank you, Derpy. I don't know why I couldn't control myself. You are the kindest pony and companion I've met. Thank you for being so kind" When The Doctor calmed down, he continued his explanations. "That still doesn't explain the Un-Tempered Schism or how Colgate became insane." Derpy waited for a response. "Ok, Derpy. You have earned explanations. The reason my race is the oldest and most developed in the galaxy is because we were exposed to the Time Vortex, the raw stream of time itself, by means of a device called the Un-Tempered Schism. Through the Schism, we could look at the Time Vortex with safety of not ripping a hole through the fabric of the universe. Sometimes the Time Vortex is too much for someone to handle and causes them to become insane. In fact, one of my dear friends, The Master, was deemed mentally ill by this, but let's move on to another subject."

Derpy asked: "Is that how she became insane? She stared into the uncovered schism?". "It's Un-Tempered Schism and no, she was born insane, but given methods to her insanity from it. One such method is that she would remove a molar from each of her victims and make a necklace once she had enough." Derpy looked at The Doctor in horror. "How can someone do that?! It isn't right!". "My thoughts exactly, Derpy, and that's why I want to find her before she discovers her true self because I believe she could be saved!" Derpy nodded in agreement. "Let's head to Sweet Apple Acres. Maybe her TARDIS is still there!"

Author's Note(Again!): I worked hard on this chapter and did not have time to go through the revisement stage as much as i wanted to. In the future, I will try to make my chapters a little shorter because i know how reading can get boring sometimes and i want to give the audience more of a calm and collected feel for my stories, instead of being bored with all 2000 words in here. As i said, i will try to cut that number down to 1500 minimum. Aside from that, i've appreciated the Constructive criticism you have been giving me, so thank you. Oh, one more thing: if you want any of your OC's in my next chapter, don't be afraid to PM me. As long as the pony isn't too complicated and unnecessary, they will star in my chapters!