Recurring Battle

by Diamendium

Rating: teen
Tags: Crossover, Dark, Human, Doctor Whooves, Sad, Lyra, Princess Luna, Changelings, Gore, My Little Pony: Friendship is Magic, Other, Romance, Adventure
Length: 4318

A visit from an old 'friend' goes in multiple directions for Lyra... She finds herself in situations and places she had never expected- With the one stallion she thought she never wanted to see again...

Lyra is always up to her business in finding out more about the humans. Their existence had finally been proven in the portal, but she needed more information. Her studies are interrupted by none other than Doctor Whooves years after they had gone their separate ways due to complications in trust. However... who would Lyra be to turn down an adventure? She reluctantly accepts, and from the time she sees his fez to the end of time itself as they witness, neither of their lives are the same. More because of the Equestrian Time War than anything else. Care to join the adventure?

Published 2015-03-05 18:50:02 UTC
Last updated 2015-03-05 18:50:02 UTC

The Visit

Oh of course it didn’t help that the moon was out! I was out all night trying to find the perfect book, and now that I am home, I can’t read it because it’s too damn dark. And I definitely can’t go to sleep, I’m just so excited to read what everypony has found out about humans. Oh it hurts to say the word. I know I am out there somewhere, in some universe as a creature with fingers… with feet, toes, a nose, and…. clothes. Alright maybe I don’t want clothes, so what? Ever since they went into the mirror. Ever since I had that dream. Ever since that lyer played the song that opened my mind… I won’t give up. I will keep searching. And when I find out what the- *CRASH!*

I stepped away from the window and turned around slowly to see the stallion. He had something in his mouth… I couldn’t identify it due to the darkness. He had something on his head, around his neck, and his wrist. None of which I could identify either. I light the candles in the room that I had refused to use to read the book. I bring them all close to the stallion, now paralyzed and with wide eyes. His mouth gaped and the thing in his mouth, that I could only assume was some sort of flashlight, fell out and onto the ground as the end of it started to make an odd noise and light up blue. The mere light from the flashlight showed the pot that he had knocked over. I brought the candles closer to his face, stepping closer to him.

“Doctor,” I start.

“Lyra,” he responds in a whisper.

“You. You promised me. You promised and you lied, Doctor. The moment that I found out about that silly-”

“LYRA! WHAT IS RULE NUMBER ONE?”

I was annoyed not only at the unexpected arrival of the stallion, but also at the fact that he had the self-given right to come into my house.

“The Doctor. Lies. And that has been proven true. I want you to tell me the truth. I want you to honestly tell me what is going on. I want you to tell me what is ON YOUR HEAD?” I indicate the red bell looking cap with tassels of some sort.

“Oh, this?” he points to the cap. “This is a fez. I wear a fez now. Fezzes are cool. Anyway, I came to tell you something, Lyra. It is something extremely important. For one, I brought you one too.” He tossed a fez at me that I caught with my magic and threw out the window. I heard a laser shot and a familiar voice saying, “Doctor you idiot!”

I returned my attention to the Doctor.

“Second, I want you to look at my hoof and I want you to do exactly as I say.”

I did as he ordered and saw that he had been writing a note. I read it with the assistance of a candle.

It said, “We are being watched. Stomp twice if you see this and follow me. Quickly.”

I walked toward him, pretending to trip and stomping twice to “regain balance.” He gives a wink and starts to walk back down the stairs after picking up his flashlight that I now realized was a new version of the once known sonic screwdriver. I gently set the candles down and blew them out as I walked by them following the Doctor. He led me out to the empty street… empty except for the blue box and the earth mare with a laser gun, and a smoking and tattered fez lying next to her.

“Hello sweety,” were the first words to come out of her mouth at the sight of us. I assumed she was talking to the Doctor.

I immediately realized who this mare was and squealed.

“RIVER! It’s been so long! Where have you been?” I frantically raced up to her. I could only expect the next things to come out of her mouth as well.

“Up-up-up-up-up! Spoilers. “

I gave a chuckle and rolled my eyes. “Of course. Well it’s nice to see you again.” I walked up to her and wrapped my hooves around her neck in a big hug. She saved my life several times and she always seemed to have more intelligence than the doctor. River was always there for Doctor Whooves too. She just seemed to be in the right place at the right time. Probably the result of the vortex manipulator that was now on the Doctor’s wrist.

“Heh heh. It’s nice to see you too, Lyra,” she responded as she hugged me back. Before it got awkward for the Doctor, I broke away.

“So… ehem… Lyra, I suppose you want to know what is going on. I came to get you for a reason. We have to leave Ponyville. We are going to stay in this dimension, but we need to go back in time to talk to Octavia.”

I looked at River for help, not knowing if I should trust him. I know that even this could be a lie and that I could be walking into some sort of long adventure that gets everypony killed. Whatever it is, I know that River can give me answers.

She gave me a nod and a small smile. She tapped her front left hoof twice. My eyes widened and I was nearly jumping around with excitement. That was our code. River and I made a code that would indicate that the Doctor WAS in fact lying, but it was a GREAT surprise. Last time that happened, we got into no danger, but spent the night staring at the most beautiful source of light that I had ever seen. Not only that, but I got to take one home. I get to now see things that nopony in all of equestria gets to see in a lifetime.

I ran to the TARDIS, swung open the doors, and jumped straight in. I was followed by River and the Doctor a few seconds later. I just couldn’t wait for whatever was coming up in my future… or my past depending on where we would. I did, however, notice that as River passed me by, she gave me a wink and whispered, “I am sure that you will have a great time. The Doctor will too,” into my ear. I already knew that. Why would he take me somewhere that nopony would have a great time? The thing that really caught my attention was when she backed into a different room and said, “You guys had better get to it. Have fun, you two.”

I was then scared to look into the eyes of the Doctor, and even more scared of what I would say next. If I couldn’t control my words, I could end up hurting him forever and making River angry. I didn’t want to do that, but I also wasn’t expecting this… assuming that what River was saying was what I was inferring… I simply walked closer to the Doctor and decided that I wanted to clarify. I refrained from looking into his eyes until I got closer to him. I was about to ask him what she meant… but as soon as I looked at his face, I knew that my question was answered.

His face was pale except for his red cheeks, and I also saw his eyes were darting around while he blinked quickly. His head fell and he was staring at the ground. I almost felt sorry for him, but I was feeling the exact same as he was. He wasn’t ready, I knew it, and he knew it most of all. I could tell that he didn’t want me to know yet, but that he had decided tonight that he would take action about it. I got the courage to speak.

“Is… is this really…. do you actually-”

I was interrupted by him looking into my eyes at last.

“Lyra. This might answer some of your questions.” He immediately pressed his lips to mine and closed his eyes. I felt like just my heartbeat alone would be able to power the TARDIS itself, and that no matter how surprised I was, no matter how wrong this felt, and no matter how angry I once was at the doctor, I never wanted the moment to stop. I had never felt this way about the Doctor, but honestly, just the moment that our lips met was all that I needed to see what he actually was on the inside. I didn’t know what to think other than, “why?”

I enjoyed it though. I know why he kissed me, but what I don’t know is why he loved me. To ask him these questions, I broke the kiss and he put up no struggle. I suppose he was expecting me to do that a long time ago. I began,

“Doctor… this… why now? Why and when did you ever start loving me?”

He chuckled. “Lyra you sure are surprised. I like that. Well I suppose it would be rude for me not to answer your questions. We started time traveling when you were younger. You are still young, but with this form, so am I. Lyra, we can travel anywhere, but you left because of the lie I told you. I never forgave myself and I probably never will. I didn’t want to lose you but losing you alive and hating me is still better than losing you in death. If I had told you that she was dead, you would not have followed me and you would be dead also. What I didn’t think about was how you would feel when Lilly wasn’t there. So I left as well. I went back to my normal dimension and I got to how I was born. Hands, fingers, clothes, two legs, and I thought of you. I thought of how I would never forgive myself and I thought about what you said to me. That brought me back here. Lyra, I looked at my hands every day and remembered what you always told me. You said, “Doctor, do you believe in pony to human transformation?” To which I always answered, “I believe that it is possible.” So I came here thinking about never losing you. How much I loved being with you and how much I realized that I loved you. To prove it…. I am going to give you hands.”

I couldn’t believe what I was hearing. Not only the fact that the Doctor decided to bring up the very thing that I left him for, but also the things that he was providing me… or at least what he said he would provide me. I just stared. I had been researching the humans for so so long and now I get to become one. I get to have hands.

“D-Doctor… how? Why? Do I also get the rest of a human body?”

“Lyra, there is something in the TARDIS that I need to show you. The eye of the TARDIS will telepathically connect you with the TARDIS itself. As a result, I can press a few colorful buttons and several wibbly wobbly seconds later, we will both be human, because I have already looked into the eye.”

“Will… will it hurt?”

“Only the fact that you will be looking into a light. Other than that, you will share all of the memories of the TARDIS and likewise.”

I couldn’t believe that it was so simple, and I wanted to do this. I knew what a normal relationship was like… but to be in a human relationship with another human will be new.

“Take me there. Let’s do it,” I requested excitedly. He just planted a kiss on my cheek and then started walking into an old room that I never took interest in. It just never seemed relevant and it was empty except for a big cylindrical object in the center of the room, and a skywalk over it. As we walked in, he pulled out some sort of a pole and slid his hoof across the edge of the cylinder. After he did so, a beam of red light came from a small hole that was invisible before. The red light soon turned into a light shade of blue and he waved me over.

“As soon as you feel your mind getting fuzzy, push away immediately, Lyra. You don’t want to stare into it for too long or else it could give you my memories as well. I do not want to put this burden on you. Just look into the light and you will be all set.”

I did as he said, slowly lowering my head forward and staring into the small hole. It wasn’t long before I felt as if my head was being pushed on. I didn’t look away though until I was seeing my memories in grey. When I pushed away, I felt like I was falling. I was only standing there looking at the wall, seeing lights, seeing old Doctors, seeing humans galore, seeing so many holes in space, so many lights, supernovas, stars, planets, dimensions, fights, battles, wars, history, aliens, and just too much. Too much. Too… much.... it wasn’t right. It just hurt. I couldn’t stop falling. Falling faster and faster and my head felt so crushed, yet so open and free. The opposite of everything I have ever known has been shown to me. Just so much impossible things becoming possible right before my eyes. I felt the Doctor’s hoof on my mane, and I turned to look at him. The small movement of my head was enough. The last thing I saw was the Doctor standing over me with a worried look, calling for River.

The Hands

The darkness didn’t go away even when I was awake. It just lingered. It seemed to taunt me and poke at me telling me to go back to my enforced slumber. I just didn’t know what to do. I guess I am now in a bed… no… I am on a couch. But I am still in the tardis. My eyes are open but even the light seemed to blacken. It was all just… dark.

I don’t hear anything. Well, other than whispers. I think that they are from the TARDIS but I do feel him. I feel his… hand. Hand. HAND. HAND? HAND! His hand was on my forehead. As soon as I realized this, I came to my senses. Everything lightened up. I felt the warmth of his hand. I saw his eyes and his blank face. I saw his clothes. I saw my clothes. I saw my hands. I heard the sounds of the TARDIS. I heard my own breath. My life was coming back.

“D-Doctor,” I began. I expected a different reaction than the one he gave, but I suppose the one he gave was better than I could have asked for. He grabbed my hand and lowered his head and our lips met. I had a different feeling than before. The first time was hard for me to catch my senses. This time, it was an explosion. Like he had hit me with some sort of weight. A weight that I loved so much and that I will never forget. I felt love. Extreme love. It was beautiful.

I felt his head move away from mine and his eyes were open. He just looked at me and I was wondering what he was looking at me about. I had forgotten about my new body until he pulled me up off of the couch.

“Lyra, you will really like this. I transformed us in your sleep. I don’t know how I look, but you are simply amazing.”

“There has to be a mirror somewhere, isn’t there, Doctor? You look amazing too.”

“Yes. But I didn’t want to spoil it for me. I wanted us both to do it together. Shall we?”

“We shall.”

He led me to a large room with a hot tub. It seemed to be a spa because it had a steam room in the back. I simply followed him into the steam room and there were mirrors in there. I looked at my face. It was just how I imagined humans looked like. The only difference was that my horn was gone, I had a nose and a mouth separate, and my skin was pale. Other than that, I realized just how little I was wearing. I guess I couldn’t get frustrated. Doctor had to dress me while I was asleep so it must have been pretty hard. Anyway, my nose was small. My lips were normal but stood out a bit. My eyes did as well. When I looked at my hands, I had 5 fingers and I could spread them out and move them into a ball. It would take some getting used to.

I turned my attention to the rest of my body. I had no cutie mark on my skin, my hair was brown but still had white streaks in it and a small hint of light green. My waist was slim and I had a chest that seemed to pop out as well as my flanks. I got worried and froze.

“Doctor… what is wrong with my chest and my flank? Are they b-broken? W-why are they sticking out like this? Th-they never did that before!”

“Lyra it’s ok. It will take some getting used to but it is normal. Trust me. I’m the Doctor.”

I turned and saw that he was looking in the mirror too. He seemed disappointed. He said something under his breath about, “same body as before.” I didn’t question it too much. I was too occupied yet worried about my own new body. It didn’t hurt to touch my chest and flank… but that was still weird that they were just poking out of my body like that.

I turned away from the mirror and looked at the Doctor. He was now looking at me. An instant blush showed on his face and I didn’t question it as I was blushing too. And we both knew why. At that exact moment, I noticed that I hadn’t seen the Doctor before that day for a long time, and we somehow were both thinking the same thing. After he lied to me, I never wanted to see him again but somehow we both got into this…. We got to loving each other in just a few minutes. I didn’t know how, something tells me that neither did he. Whatever it was, I enjoyed it. No matter how strange it was, I enjoyed it. However, I somehow knew that River would be disappointed in the fact that we weren’t snogging all over the place. I blinked and looked down, but his gaze remained on me.

“Lyra, I really-”

“I know, Doctor. It isn’t normal for me, and I don’t know about you, but I am sure of what I feel about you, no matter how quickly it came.”

He didn’t try to respond. I was the first to break the long silence. “We should probably go sit down, I haven’t stood like this before. Besides, I think we have a lot of catching up to do.”

With that, he grabbed my new hand, which felt interesting considering I had never felt that before, and he slowly began walking toward the same couch that I had woken up on. I welcomed his warm hand in mine. It was almost like a little hug. I like hugs.

As we both sat down, he gazed toward the center of the tardis. As if something were standing over there. However, there was nothing. His avoiding my eye contact was to be expected, and I did the same, letting my head hang and my eyes lock on the ground. It was a couple minutes before I spoke. It seemed that he had always been waiting for me to speak.

“So…. what was it you said earlier about us being watched? In my house?”

He did turn his head, but he remained silent for a few seconds.

“I know something that nopony else does. I try… so hard to keep it a secret for the safety of many and for the tranquility of the near future in Equestria. When I tried to come and see you earlier tonight, I got stuck in a time warp. Nothing was right. The time itself was confused. It didn’t know whether to go forward or backward or stand still.” He let out a sigh and held my hand. “Time showed small segments of the past and the near future of where I was. I happened to be outside of your house. I saw fire. I saw changelings. I saw evil. I saw…. you. I had to watch you helplessly. You…. you jumped off of your roof. Into… into a fire, Lyra.” His eyes were watering, and it was quite obvious to me that he wasn’t lying. It was the truth.

“Wh-what does that have to do with being watched…?”

He wiped his tears away and took a deep breath.

“BonBon…. your roommate. She knew I was coming apparently… because she was outside of my tardis when I finally got free. She was just as pleasant as I remembered her… but it wasn’t her. Lyra, she was a changeling. The invasion has already started. I knew she was a changeling because…. when I made her laugh while we talked, it was a cackle. When she looked straight into my eyes, they flashed a bright green. Furthermore, my contraption that goes ‘ding’ went off as I opened the door.”

I was dumbfounded. I didn’t know what to think…. First off, a contraption that goes ‘ding?’ Furthermore, he watched me die? Kill myself? He watched a war in Equestria? That just didn’t sound good. None of it did. If there was going to be hope, something would need to be done. Quickly. But I didn’t want our time together to end, no matter how crazy the situation was. We were in a damned TIME MACHINE. Did it really matter how quickly we got there if we can get there any time we want? I decided to express my thoughts.

“Doctor… Wh-what about this? Right now? Us being together? We can go any time we want, right? I mean… with the tardis being a time machine and all…” I said shyly, hoping for the best response. Honestly, I didn’t want to come across as selfish, only wanting the Doctor and not caring about my own planet.

“That depends. According to my calculations previously, the time warp goes on and off. It is a disruption of the fabric of time simply because of frequent time and interdimensional travel as of late. I suppose it could be from changelings or from other forms of interdimensional transportation in Equestria. That means, it will be going on and off in waves. They can last minutes to milliseconds. The timing of our travel must be perfectly timed. We can choose to go any time we want, but the wave must be at a low to where by the time the tardis reaches the area, it will not get trapped in a time warp.”

From what he had said, I understood only the fact that it went in waves. Timing would have to be perfect. If not, we can get trapped again. Alright that is simple enough.

“W-we can leave any time? So does that mean… we can stay here? Until we choose to leave? I want to stay with you as long as I can, Doctor. I want to make sure that we make the most of this time in case we don’t make it back from the…. Equestrian Time War.” I knew about the time war of his own on his home planet. This time, it was the same. As far as we knew, there can be more than changelings. Even if not, changelings will be far more than enough to destroy Equestria if they so please. It was the equine equivalent to the time war. I’m sure he knew it as well as I.

“I would love to stay with you here, but only for a while. Lyra, you must understand that this is serious. If we don’t stop it at the source, the battle will become what we both know could happen. Nobody expects it to come. If we cut them off, we can win easier,” he explained. I knew it was the truth. He was never wrong when it came to serious things.

Hesitantly, I responded. “Alright. Why don’t we get it taken care of as much as we can. I love you, Doctor. I trust you now,” I said softly before kissing him softly yet again. It wasn’t as special this time, because I knew it was a kiss that could be final. A kiss that would be the last one if the war was as expected.

With that, he kissed back a small bit and we both pulled away at the same time. He stood up and slowly made his way to the control panel. “River! Open the armory!” He glanced at me as I stood up, walking to him. He turned a few knobs, flipped switches and cranked gears.  With that, he put his hand on the lever. “Hold on tight, Lyra.” He said with a massive grin. “We have a war to win.” With that he held onto a railing with his other hand. “ALLONS-Y!” He threw the lever. Everything around rattled and whirled, and with no further warning, we were on our way to the Equestrian Time War.