Rainbow Dash awoke, still in the cave, but without any sign of Celestia, Luna, or a fire. She shivered a little. Without the fire the cave had grown quite cold.
She stepped outside and shielded her eyes from the bright sun. After her eyes adjusted she looked around at Canterlot. She was on the far West side of the city, the cave hidden in a back alley behind a building. The castle seemed to be mostly the same as she remembered it. She flew up to get a better look around.
Once in the air she noticed something strange. All the ponies she saw were in guards uniforms, there were no citizens walking around. She flew down to meet a small group of guards. “Uh, hey guys... I'm a little lost, can you tell me where I am?”
The guards stared at her for several seconds in stunned silence, until one of them yelled. “Seize her!!!” They all jumped on her at once and she couldn't get away. After having her front hooves chained together and her wings tied, they began to march her towards the castle.
One of the guards looked at the one who had yelled. “Uh, Captain? Where are we taking her?”
The captain frowned. “I've had orders from Princess Luna to capture any pegasus we found with rainbow hair and bring them to her.”
“So she has been expecting this one to show up?”
“Yes, apparently.”
They made their way to the castle slowly, impeded by the chains around Rainbow Dash's front legs. At the front gate Rainbow Dash spied two flags, one on each side of the door. They had Luna's cutie mark on them instead of the flag of the two sisters.
After the guards of the front gate checked the paper work the captain was carrying, they brought Rainbow Dash before Luna. Luna was once again in her familiar alicorn state, and was sitting on what appeared to be Celestia's normal throne. When she saw Rainbow Dash she smiled broadly. “Release her from those bindings at once Captain.”
The Captain looked first at Luna, then at Rainbow Dash, obviously not wanting to free his captive. Hesitantly, he untied her wings and then released the chains on her legs.
Rainbow Dash took to the air and folded her front legs. “What's the big idea having the guards tie me up like that Luna?”
“I apologize dear Rainbow Dash, I wasn't sure what state you would find my dear city in when you arrived. The orders to capture you were standing.”
“What do you mean what state? Is something wrong?”
Luna looked over to the guards. “You three may go now.”
They bowed and walked out of the room. Once they had left, Luna turned back to Rainbow Dash. “Yes, there are many things wrong. We are frequently attacked by many of our foes. It is not often we have a week of peace.”
“Foes? Like who?”
“The tyrant Discord has plagued my city for nearly a thousand years now.”
“Discord? But he... he should be stone.”
“Stone? Is that what the future holds? How is it that we turn him to stone?”
“With the Elements of Harmony, that's what we used, and what you and Celestia used.”
Luna got a sad look on her face. “I see, I was afraid you would say something like that. Still I'm at least glad to hear he is not undefeatable.”
“I don't get it, why can't you and Celestia just use the Elements on him?”
“The reason is two fold. Firstly I'm unaware of these Elements of which you speak. Secondly...” She paused, looking away from Rainbow Dash. “Secondly... Celestia has not been with us for quite some time.”
Rainbow Dash stared at her, dumbfounded. “When did... how could...?”
Luna shed a small tear. “It was not long after our ascension to being alicorns, as you had predicted, that the tyrant Discord appeared. At first he was a nuisance, but he quickly became a serious problem. I tried to reason with her, tried to strategize, but she wouldn't hear of it. She said that until the day we saw you again, we were invincible. Your prophecy foretold us becoming the rulers of this land, and until it was met, we were destined to succeed. She charged headlong into battle with Discord, taking no heed to my cries. She fought hard with him, but was unable to beat him. In a final desperate attempt, she summoned the power of the sun to her aid. She couldn't control the immense power of the sun, and it quickly killed her, but in the process she greatly injured the tyrant. He escaped before I was able to finish him, but since that day he has grown slowly more powerful. I fear that he will soon regain his full potential, and we will be unable to stop him.”
Rainbow Dash stared at Luna for several minutes, thinking about everything she had just been told. History had changed dramatically. There were no Elements, Discord had never been turned to stone, and worst of all Celestia had been dead for nearly a thousand years. She took a deep breath, then exhaled. “So how can I help?”
Luna smiled. “I'm glad you asked. Today is the day we finally strike back. My troops have been doing serious reconnaissance for months now, and my scientists tell me that they have finally finished building a weapon that may be able to stop Discord. The problem is... powering the device seems to be nearly impossible.”
“OK... still, how can I help?”
“You might find the unique nature of the device intriguing. It is designed around the concept of temporal manipulation. I had thought long and hard about everything you told me so long ago, and I decided that the best way to beat Discord, was to stop him before he got started. My scientists worked for years building a device that can destroy anything by stopping it from ever existing.”
“Wow... how is that possible?”
“It wasn't, without you. You can help us power the device. You know where the rocks are that gave you your power. We can use them to power the machine and defeat Discord.”
“So you want me to lead you to the rocks?”
“Yes. Is that a problem?”
“I guess not, its been like four or five days, and I have only been there twice. If it hasn't changed too much I might be able to find them.”
“Splendid, I will fetch the head scientists at once and we will leave as soon as we can. Wait here please.”
Luna went and fetched the scientist and several pegasus soldiers to help carry him and the small device. They all made their way to the Everfree Forest. After flying for ten minutes, Rainbow Dash spotted the clearing where the rocks should be. “Down here!”
The team landed with the doctor and the device. Luna landed last and looked around. “So where are they?”
Rainbow Dash walked over to the large rock and kicked it out of the way. “Down here.”
Luna, the doctor, and several soldiers looked down the long hole. “Right.” The unicorn doctor said as he made his way over to his weapon. The weapon itself was actually very small. About half the size of your average pony. He levitated it into the air. “We will need to go down there with the device.”
Rainbow Dash nodded and jumped into the hole. Luna looked to the soldiers. “Wait here, make sure no one follows us.” She then jumped in after Rainbow Dash. Finally the doctor, still telepathically holding his device, jumped in behind them.
Once inside, they looked around the cave. It still held the purple glowing rocks as it had before. The doctor walked over and picked one up. “Fascinating, I wonder what gives them their glow?”
Rainbow Dash laughed. “Good luck egg head. My friend Twilight is a genius, and she couldn't figure it out.”
The doctor huffed, and then set down his device. “Well in that case, let us get started.”
He reached down and hit a small button on the little cube-like weapon. It began to hum loudly.
“What are you doing?” Rainbow Dash asked.
Before he could answer, a small ghost like image appeared in front of them. The doctor reached down and adjusted a small nob. Slowly it became clearer. It was Rainbow Dash.
“What in Equestria.... what are you doing?”
Luna smiled broadly. “A little more doctor.”
He moved the nob ever so slightly, and the other Rainbow Dash came into focus. The second Rainbow Dash looked around at them. “What in the hay? Who are you?”
Luna raised her horn and completely engulfed the second Rainbow Dash in magic, and before either Rainbow Dash could do anything, Luna destroyed her.”
Rainbow Dash sat there and stared, unsure of what just happened. The doctor began to jump up and down in obvious glee. “I got it. The paradox is complete!”
Rainbow turned to him angrily. “You mean your plan was to kill me this whole time? Or, kill the other me?”
Luna stepped between them. “I'm afraid it was the only way to power the device. Securing a paradox fractures the time line you see. Now this device exists because it isn't supposed to. Now it can do anything.”
The doctor stepped forward. “That is more or less correct. You have been creating so many time lines, always jumping around, back and forth, I bet you never even stopped and thought about what had happened to them, had you?”
“Well... no, wouldn't they just stop existing?”
“Incorrect! Those time lines continued after you left them, you simply can't go back to them. Using this device, I have taken one of the universes you had made from jumping around and used them to fuel it. It now has the potential of an entire universe all rolled into one weapon!”
Luna took a step forward. “This was necessary to our survival, I hope you understand, Rainbow Dash, that this was the only way I could protect my people from the tyrant Discord.”
“You murdered all of those thousands, no billions, just to save a few?”
The doctor shook his head. “Murdered is such a cruel word. We merely stopped them from existing. They felt no pain.”
“That doesn't justify what you did.”
Luna laughed. “I don't need to justify myself to anyone! What I do, I do in the name of peace and sanity! And do you know what? I don't need you anymore.”
She raised her horn and engulfed her in magic. The doctor shouted. “WAIT!!!”
Luna looked at him impatiently. “What?”
“You can't destroy her, don't you see? She IS the paradox. We need her. Nothing else from that universe remains except her. She exists outside of time, and as long as she does, the paradox remains intact.”
Luna looked at Rainbow Dash, frozen in the air, still completely contained by her magic. “How can we possibly contain her?”
“We don't need to, we can just get rid of her here.”
“Make up your mind, can I kill or not?”
“Not kill, but I can trap her in another dimension, completely out of our way.”
“I see, but there is one thing you are forgetting doctor.”
“Oh?”
“I helped you build that machine. I don't need you anymore either.” At that, Luna picked him up and crushed the doctor into dust, just as she had the past Rainbow Dash.
Rainbow Dash tried to move, tried to break free. Luna laughed as she walked over to the device. “All the power in the world, the ability to move through time itself, and now look at you, helpless. She reached down and hit several buttons on the machine. A small hole opened in the air, solid black and perfectly circular. “Have fun!” Luna threw Rainbow Dash through the portal, and it closed behind her immediately.
Rainbow Dash turned around to see the portal had vanished. She looked around to see where she was. It was a large plain, as far as she could see, with a few scattered trees. Overhead the sun sat perfectly in the middle of the sky. She shot off in a direction, hoping to find something, anything.
Hours went by, she continued to fly. After ten hours of nonstop flight she landed next to a tree. She looked up at the sun. It still had not moved from the center of the sky. She laid down under the shade of the tree and began to cry. What had she done? How could she fix this? She continued to cry until she eventually passed out from exhaustion.