Prologue
"I can control the Sun and the Moon; but why do they hurt? Doctor, why do they hurt?"
-Bad Wolf
That metaphor haunted The Doctor, who didn't understand it's meaning until he came to Equestria. When he travelled alone, he would research on the Night and Day cycles the two princesses had control over here. The minutes he spent researching turned into hours, and the hours turned into days. Derpy Hooves eventually became concerned about his well-being, so she did the only smart thing she could think of and requested an audience with the princesses themselves. Denial after denial came through, until one day a letter arrived that read as followed:
"Dear Derpy Hooves,
I, Princess Celestia along with my sister, Princess Luna have received the many requests to be granted an audience with us. As much as we wish to help you in the matter that has arisen, we simply cannot have you come to Canterlot. A threat has been claimed on our lives and we must take every precaution to prevent our untimely deaths."
With much sorrow and regret,
Princesses Luna and Celestia
P.S. On a more private note, we are fully aware that you are a companion of The Doctor, and it has also occurred to us the request for our audience was to seek help for whatever danger he is in. Listen, whatever is wrong; please try to seek help for The Doctor as much as you can.
After reading the letter, this gave Derpy an idea. "Tomorrow, I'll go to the library and see if Twilight is there. For now, I'm going to find out what he's been researching this whole time" the mare thought to herself.
The next morning, in the TARDIS…
"Doctor, are you in here?" She said as she was approaching the library. When she approached the doors, Derpy could hear mumbling of some sort and slightly opened the door. As soon as she did that, the mumbling stopped and she heard somepony get up from a chair and walk towards the door. "Doctor, I'm very worried about you." She paused for a moment, expecting a reply, but there was none so she continued. "It's been days since you first went in there." Derpy opened the door all the way this time, and before her stood The Doctor, but with a dirty coat, baggy eyes, and ruffled mane. She would have never recognized him if it weren't for his golden eyes, gazing with hope stronger than ever. "Not to worry, Ditzy!" The Doctor said "My name's Derpy…" "Right, Ditzy! What I've been doing in here is researching something important and I think it corresponds with your rulers' ability to raise and lower the sun and moon. Now if I only had the proper books…"
Derpy got a brilliant idea to get The Doctor to come with her to see Twilight Sparkle. 'if I can convince him there are better research materials at the library in Ponyville, maybe he'll come with me and we can talk about what it is that's so important that he had to abandon Me, Dinky and the rest of his friends'. "Doctor, maybe there's a book in the Ponyville that can help you with your research!" She said. "Great idea, Ditzy! Let's go ask Twilight if there's anything that can help us find what I'm looking for." "Oh, it's Princess Twilight, now. You probably don't remember because during that time we had to hide your identity from the Krillitanes." So the Doctor and Derpy went to the library, which would be the start of a path neither of them could predict; One that would change their lives forever.
A few moments later at the Ponyville Library…
"Derpy, I'm glad you came by! You said there was something wrong with the Doctor, right?" Twilight asked. "(In a hushed tone) keep your voice down! I convinced him there were research materials on the sun and moon cycles here; He doesn't know why I really brought him. The Doctor's in a bad state, Twilight. Just look at him! His mane is knotted up and his coat looks like it hasn't been washed in months! Please try to help him, okay? For now, let's keep up the act to bide us some time." The purple mare nodded in agreement. "I have the materials right here for you Doc-" Suddenly, The Doctor became giddy when he saw the new wings Princess Twilight adorned on her back "You're an Alicorn now! How is that even possible?! Does your species have a sudden evolutionary change, and why are your wings angled? You must be considered a princess now! You should get a cane with your face on it! I think it would be the most hilarious thing I would ever see!" "Even his attitude is stranger than usual. I have no idea how to help him in his current state! Maybe if I just tell him about Derpy being concerned, maybe he'll explain. After all those two ponies have been through together, I wouldn't doubt his loyalty to Derpy." Twilight thought to herself. "Doctor, Derpy is concerned about you! You've been in your TARDIS for months on end, not leaving even once to take a break!" "Don't be ridiculous, Twilight! It's only been a few days!" The brown stallion responded. "LOOK AT YOURSELF! Your mane is as tangled and unkempt as the Everfree Forest, your coat is a completely darker shade of brown, and you've almost made little to no sense as soon as you walked in!"
After Twilight's rant, The Doctor finally came to his senses a little and took a few minutes to look at himself in a nearby mirror. He was shocked at the stallion staring back through it. "Twilight's right. What few days I spent in the TARDIS must've been months out here!" After examining his unkempt self, The Doctor bowed his head down sorrow and began to apologize. "I-I'm sorry, I wasn't aware that it's been that long. When you spend a lot of time in the TARDIS, a few hours could feel like mere seconds. Honestly, I didn't know how long I was actually in there." After hearing this, Twilight regretted yelling at him the way she did and apologized as well. "Now that you've come to your senses, could you tell us the reason behind your research? What's so important about the sun and moon cycles?" "Before I came to this planet, there was a friend I had. Rose Tyler was her name. One day while we were travelling, we were trans-matted onto different TV game shows on a space station, which was controlled by Daleks secretly. In order to save everyone, Rose looked into the Time Vortex itself, gaining god-like powers. This transformed her into Bad Wolf- an incarnation of the Vortex with a desire to help, no matter what the cost." The Doctor said. "Isn't that a good thing, though Doctor?" Derpy asked. "The problem is no one person can have that much power coursing through them, not even Time Lords such as myself. So, in order to save her, I had to take that power within me and give it back to the TARDIS, which acted as a conduit of that energy; That's how it travels through time and space. The few seconds I had that power coursing within me was also enough to nearly kill me. That's when I regenerated for the 10th time." Both mares listening to this story began to understand why the TARDIS was a dangerous thing if an enemy got a hold of it. "Before I took the power away from Bad Wolf, she said something that's been itching at me ever since I came to Equestria." "What did she say, Doctor?" Both ponies asked simultaneously. "'I control the sun and moon, but why do they hurt?' For 80 years, that quote was meaningless to me, just an echo from the past, but now I get it! There must be something that's going to happen to your princesses and I think the day and night cycles might have something to do with it." "*gasp* I just realized, Doctor! Before I came to get you, I received a reply letter from the Princesses and it said there was a threat made on Canterlot." The Doctor had a smile on his face after hearing this. "Then what are we waiting for? Let's Go!"
