The sun rose, and Nightmare Moon faced her older sister. Celestia looked forgiving, and the words she said was just as well. "Luna, this isn't you. We can talk about this, please-"
"NO! I will fight against you, I will fight until Discord rises again. I will not surrender in a thousand years."
"Then I have no choice. Believe me when I say I am so, so sorry. I, Celestia, Princess of the sun and day, banish Luna, Princess of the moon and night, to the moon." The elements glowed as Celestia spoke her spell. Luna's body flickered, and was gone for a moment. Then, Luna came back. But this wasn't Nightmare Moon, but Luna, the Luna that Celestia had always known, the Luna that Celestia loved and cherished and hoped for in his hellish battle. Luna was still defiant, but she looked more accepting, as if she knew this punishment was coming for a long time. Celestia wondered why this happened, but she had no time to consider it, because the first element, generosity, fired a bright bolt of light at Luna. Then Honesty, loyalty, laughter, kindness. And then, the final element fired at Luna-the element of magic.

One thousand years later, Twilight Sparkle and five other ponies used the elements one more, changing Nightmare moon into her other side. She was Luna, Princess of the moon and night, once again.

Fast forward a few years more, Nightmare Moon would rise again...
"So, how does the TARDIS work again?"
"I told you, Ditzy."
"Doctor, wibbly wobbly timey wimey doesn't really cover a machine that can travel in time and space."
"Well, It's as good an answer as any. If I really explained it in the long version, it would take three hundred years to do it. And I should know, getting Epsilon the academy exam back on Gallifrey.
"Epsilon? What's that?"
"Oh, instead of grading with A, B, C, D, and F, we used greek back then. There was alpha, beta, delta, epsilon, and omega. So, Epsilon was pretty poor back the-"
There was a loud BANG, and the TARDIS crew fell down. The TARDIS was rolling around in the time vortex, like a child's toy.
"Doctor, what's happening?"
"Something-or somepony-is trying to take control of the TARDIS! Here, I'll try to minimize the impact..." and he set to work on flicking switches and pulling levers. Soon, the bouncing stopped, but Ditzy could feel that the TARDIS was still moving. "Doctor, you haven't wrestled control yet."
"I know, Ditzy. Let's see which fine fellow wants to take our TARDIS, why, and most importantly, how!" Just as the Doctor finished his sentence, the TARDIS materialized. The Doctor opened the TARDIS console, which showed a desolate landscape, grey, but the sky was shining with stars, and had one planet. The Doctor said "Alright, Ditzy, I've got good news and bad news. The good news is that the TARDIS materialized and we know where we are. The bad news is that our friend has a strange obsession with chinese baking goods, Jarlsberg cheese, and moon pies."
"Which means..."
"We're on the moon."
Ditzy uttered some choice curces. "When are we, Doctor?"
"Oh, we are in-oh, shit."
"What, Doctor?"
"The year is 100 ANM [After Nightmare Moon]!"
"So?"
"DITZY, DON'T YOU UNDERSTAND? WE ARE ON THE MOON AND THE ONLY OTHER LIVING ORGANISMS THAN MYSELF ARE YOU AND A PSYCHOPATHIC PRINCESS!"
"That's not good."
"No, that's not good. And I have a feeling that Nightmare Moon is the one that brought us here."
The Doctor strode over to the TARDIS doors, and opened them. Staring back at them was Nightmare Moon. Ditzy grabbed the Doctor's sonic, to close the TARDIS doors and lock them. But Luna was already inside, and blasted the sonic out of Ditzy's hand. "Luna, stay away from my TARDIS."
"Doctor, you do not know why I brought you here. I simply wish for you to take me to Equestria, where I can challenge Celestia once more."
"I can't do that, Luna. You haven't changed your psyche. If you don't wait 900 more years, then you will just make eternal night. Again. We're from the future, so we know how this will play out." But Luna just stepped onto the TARDIS, and her horn glowed. At once, the TARDIS began shuddering.
"Luna! You need to get off this TARDIS. It's trying to shake you off."
"I have elemental power over celestial objects. You have a time machine. What the hell, let's go kill Celestia." The TARDIS, trying to shake Nightmare Moon off, started going forwards in time, landing at the year 1003, in Canterlot. While in the TARDIS, the doctor yelled "LUNA, PLEASE! BY THE YEAR 1000, YOU WILL HAVE BROKEN FREE FROM THE MOON. IF YOU ARE THERE, AND ANOTHER LUNA WILL BE THERE, IT'LL CREATE A TEMPORAL PARADOX THAT WILL RIP A HOLE IN SPACE AND TIME THE SIZE OF THE EVERFREE FOREST! DON'T DO THIS!"
But it was too late. The TARDIS had materialized in the worst possible place: The Canterlot throne room!
The Doctor, Ditzy, and Luna2 stepped out in the throne room. There, they saw a thunderstruck Celestia, and a confused Luna.
"Um-this isn't what it looks like?" asked the Doctor. The guards advanced on the three, but Celestia said "Stop. Luna is right next to me, and Luna is right there. I would like an explanation."
The Doctor explained everything-the TARDIS flying off, getting assaulted by Nightmare moon, and coming back here. Celestia though this over and said "I believe you. But now we have to deal with a second, psychotic Luna. But where is she? Then the sky was darkening. Celestia struggled to keep the sun up, and Luna struggled to keep the moon down again.
Luna yelled "You have to send for my second self and defeat her! Celestiaspeed, Doctor!" The Doctor and Ditzy ran towards the TARDIS. the tardis was not bigger on the inside, but had the inside shape of a normal box it's size. the docotr opened his eyes wide. "Oh, dear."
"What happeded."
"when nightmare moon came, and luna was in the same room, it caused a temporal paradox, that could threatened the entire universe!
They ran out of the throne room, and into the darkness. "Think, Ditzy." said the doctor "When Twilight and her friends defeated Nightmare moon, where were they?"
"Where the elements were used for the first time in a long time, in the ancient castle of the royal pony sisters."
The Doctor couldn't help but giggle. "I thought it would actually have a name?"
"Well, it is in the everfree forest, if you want to find where it is."
The Doctor reached into his saddlebag, and pulled out a wristband. "Mobile teleporter. I know it seems redundant, but it will be just what we need."
"Doctor, we need more than that. The only way we will be able to defeat Nightmare Moon is by using the elements of harmony.
"Alright."
"But only a few people can wield them."
"Which would be Twilight and her friends, no?"
"Yes, it is Twilight and her friends. But we don't have enough time to do that."
"We've got to. as long as Luna doesn't go unstable in her efforts to keep the moon up, then we have enough time."
"Wait. I've got an idea. Lets go to the everfree forest. We might be able to get some answers. "Wait-there's some temporal distortion. I can't get there with a teleporter. We'll have to get there on foot."
Once in the everfree forest, they rested. Then, there was a rustling in the trees. The Doctor and ditzy looked around, and the doctor pulled out his sonic, and started scanning. then he opened his eyes wide. "Ditzy, run! Just run!" They ran, and 20 Reapers followed them. "What are those, Doctor?"
"Reapers-creatures of the time vortex. I've met them once before. They appear only in a temporal paradox."
The Doctor fired a bolt from his sonic. One Reaper fell back into the time vortex, screaming. Then, they jumped into a bush. a Cocatrice came up from the bush, and turned the next reaper into stone. The doctor and ditzy fought Pugh the reapers, but more arrived on the scene. The reapers fought them all the way to a stone wall When they felt the cold stone wall of the castle, the Reapers started flying away "Hey, why are they all flying away, into the time vortex?" asked the doctor, but his question was not answered. "Doctor" said Ditzy. "We're here." Above their heads loomed a spire. "Yep." said the Doctor. "So we are.". They walked in the great double doors of the castle, and they were faced with two pegasi, their heads lowered to the ground. The Doctor gasped. Then he screamed. Why? Because the pegasi were made of stone. "Don't blink, Ditzy. Just don't blink."

The doctor was about to run, but then he thought. "Listen." he said, his tone was as dead as a corpse. "I don't know how you got here, but we can come to some sort of agreement."
The walkie-talkie in the Doctors saddlebag spoke: "What would that be, Doctor?"
"Alright. I'm talking about absorbing 1003 years of time energy."
"Why would you want us to do that?"
"Have you noticed the reapers? Theres been a temporal manipulation, and I need you to touch the pony that got into the future."
"Alright, we will."
"Give me your word that we or any other pony other than your target will come to no harm."
"You have our word."
The four made it back to Ponyville. The Doctor kept his eye off the pegasi, so they could follow. nopony else looked at the pieces of stone, for they were all stuck at their homes. nevertheless, the doctor took a short break to make sure the pegasi had not gotten another victim. eventually, the foursome reached Canterlot. "Where's Nightmare Moon?" asked the doctor? "In the Lunar tower, where she rises the moon. Don't worry about Luna and Celestia. We've got them to safety." answered a guard. they rushed to the lunar tower, where guards were. They were ramming the lunar tower doors with a battering ram. Some unicorns were using magic to blow their way in. The doctor confidently aimed the sonic at the lock, and the door blew open. they found Nightmare Moon, using her magic to raise the moon. "Bring her down!" yelled the guard captain. There was a rush of earth ponies, crossbow bolts, and magic spells. There was much shouting, as the doctor kept an eye on the pegasi. When the dust cleared, all the ponies lay on the ground, and the only thing between an everlasting night and equestria was the Doctor, his companion, and two stone pegasi. Nightmare moon had no choice but to laugh, but shut up when the Doctor said "Laugh all you want, but you will be laughing on the moon very, very soon Luna. Pegasi, please get the lights." The lights flickered off, and Nightmare Moon noticed that the stone pegasi had moved, and were in a more sinister position. The lights turned off and then, something happened. Nightmare Moon changed into Luna. The Luna that the Doctor had met in The throne room, the Luna from today. Luna looked at the Doctor. "Tell tia that I was sorry." she said. And then the lights flickered, and Luna was gone. The Doctor smiled. "Well. I think I want to give a big hoof to our Pegasi of the night! Little do they know that it's their last one, Ditzy."
"Doctor, I know what you mean. You can't do this. Let them live. Please."
"Ditzy, I can't let them live. They are the weeping angels. They are quantum locked. They can't move while they are seen. If they touch somepony, they throw them back in time, and feed off the life energy that you would have lived if you had not been touched." He reached into his saddlebag, and fired at the angels with his sonic. It pulsed a large frequency, and soon, the angels began breaking up. Then, they exploded. the guards were regaining consiousness. The doctor went to one of the guards and told him: "Tell celestia that Nightmare moon was gone now. It's safe. And Luna just wanted to tell Celestia...She's so sorry."
When the news reached Celestia, she went up to luna, and asked "You knew?"
"Of course I knew."
Celestia could have done many things-she could have yelled at her sister for not telling the Doctor, but she knew it would cause a temporal paradox. but nevertheless, she felt it was appropriate to hug her sister. "I'm so glad you're back, Luna. Don't ever leave me again."

One thousand years ago, as a result...
"Then I have no choice. Believe me when I say I am so, so sorry. I, Celestia, Princess of the sun and day, banish Luna, Princess of the moon and night, to the moon." The elements glowed as Celestia spoke her spell. Luna's body flickered, and was gone for a moment. Then, Luna came back. But this wasn't Nightmare Moon, but Luna, the Luna that Celestia had always known, the Luna that Celestia loved and cherished and hoped for in his hellish battle. Luna was still defiant, but she looked more accepting, as if she knew this punishment was coming for a long time. Celestia wondered why this happened, but she had no time to consider it, because the first element, generosity, fired a bright bolt of light at Luna. Then Honesty, loyalty, laughter, kindness. And then, the final element fired at Luna-the element of magic.