The prison was meant to last eternity, but not even bonds forged by the Elements themselves could contain an alicorn forever. As the centuries passed and Nightmare's magic slowly returned to her, she turned it upon the seals that held back the majority of her power. It took years and years of constant assault, but the seals slowly began to fail, one by one. Finally, enough seals had been destroyed that that she was able to project her magic outside of her prison. She reached out with all of her hatred and range for Celestia's sun. The energy she siphoned from its destruction would augment her own, providing power to assault the final seal.
Her aura touched the sun and winked out of existence. Cursing, she cast another spell to find the reason behind this outrage. She could see it now, Celestia, always planning ahead, had protected her sun. Nightmare Moon would have to expend far too much energy to get past Celestia's protection, in the end she wouldn't have enough to break the final seal. Still, Celestia's sun was not the only star. Nightmare had a whole sky of them, and they would aid her in her escape.
She searched the heavens and found the largest star within her grasp. She cast a spell gathering the full output of the star, and concentrating it into a radiant beam of energy, which she then used to augment her magical attack. There was no effect, the final seal was the strongest of them all and would not be destroyed as easily as the others had.
Frustrated, she added the output of another star, and another, and another, until she had concentrated the output of 16 stars into one massive attack. It was then that she detected an almost imperceptible drop in the seal's strength. Now it was just a matter of time before it fell. And there was one more thing she could do to speed things up.
Nightmare Moon's horn shone with a fierce glow, and the output of her attack grew immensely. Time itself bent to her will as the stars burned faster and faster. For each second that passed by, each of the stars experienced hundreds of years. It would be almost a year before the last one burnt itself out, but the seal would fail by then.
After a year of constant assault the final seal was cracked and broken, it could no longer contain the dark alicorn. The last star had finally died, but she did not need them anymore. Her horn flashed and a pulse of energy expanded outwards. It hit the damaged seal which exploded, shattering into tiny shards of magic that then faded out of existence.
For 1000 years she had been imprisoned. Even to an immortal such as herself, it was a long time. In the back of Nightmare Moon's mind, a tiny part of her brain had wished for a death that could never come. For 1000 years she had been starving, for 1000 years she suffocated aon the airless rock that was her prison. The harsh heat of day scorched her flesh, while the bitter cold of night turned her blood to ice. But she endured, driven by rage and the need for revenge against her sister and the desire to force all of pony kind to love and worship her.
Nightmare Moon looked up at her home world floating in the depths of space, she stretched her wings, rising off the lunar surface, her horn lit with a dark power. In a bust of magic, she disappeared.
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Celestia could feel Nightmare Moon straining against her prison. It would not hold her for much longer. She knew this day would come and it both frightened and excited her. If everything went according to plan, she would have her sister back, but she knew that there was much room for error.
A letter popped into existence in front of the princess, it was from her student, Twilight Sparkle. She had a good idea of what the contents would be about. Twilight was a smart pony, and Celestia has given her all access to all the knowledge she would need to put together the puzzle of Nightmare Moon. She opened the letter and skimmed over the contents, confirming her suspensions. Twilight had read the prophesies, as Celestia knew she would. She was was worried about the Nightmare's return.
For a moment, Celestia considered telling Twilight the details of her plan, but then she reconsidered. The plan was a dangerous one, if Nightmare Moon found out what Celestia was up to, Twilight would be killed. The chances of failure was high, but it was the only way to save Luna and end the Nightmare. She sighed, and picked up her quill and began to write a response.
My dearest, most faithful student Twilight. You know that I value your diligence and that I trust you completely, but you simply must stop reading those dusty old books!
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Nightmare Moon had expected far more resistance from Celestia. Here she was, ready to enact her revenge upon her sister, ready to plunge Equestria into eternal night and Celestia hadn't even shown her face. Nightmare Moon could feel Celestia's presence in the distance, she followed it to a small town, but no matter how far she pushed forward, Celestia kept backing away. All she found in the town was a gathering of ponies waiting for Celestia to raise the sun.
It was then that she sized control of the heavens, a move she was sure would draw forth her sister. She banished her sister's sun from the system, sending it hurtling off into space. But Celestia still did not come forward. In fact the only opposition Nightmare Moon had faced was some insignificant little unicorn.
"I did. And I know who you are. You're the mare in the moon, Nightmare Moon," Twilight said.
Nightmare Moon quickly left the town hall after that. She knew Celestia would not run forever, there would eventually be a conflict and that meant only one thing.
"The Elements," Nightmare Moon said to herself. "She must be gathering the Elements."
Nightmare Moon had no intention of spending another 1000 years imprisoned so she had planned for this eventuality. She had not spent the last 1000 years blindly chipping away at her restraints. She also studied the ancient magic of the Elements and had come up with a counter spell that she was sure would protect her. Still, if she could stop Celestia from collecting them, it would greatly tip the balance of power in her favor. Perhaps she could even destroy them.
Nightmare Moon cast a detection spell. The raw power of the Elements should have made them stand out like a light in the darkness, but she was only getting a vague feeling of where they might be. Celestia must have found a way to hide them. She opened her wings and took to the sky, flying towards the dark forest on the edge of town. The landscape had changed in her long absence, she did not recognize where she was but there was a small hint of familiarity. Reaching out she felt a great rift at the center of the forest and she realized where she was. This forest must have grown up around the very place she and Celestia had fought a millennium ago.
Only the great battle between her and her sister could have twisted the fabric of reality in the way she sensed. Based on what she sensed, the Elements may still be at her former castle. Now that she knew where she was going, getting there would be much easier. She cast a teleport spell and disappeared.
Only to reappear in the exact same location.
"What is this?" she thought.
Teleporting to the castle should be trivial, unless... unless Celestia was blocking her. That confirmed it then, it must be the location of the Elements, why else would her sister do such a thing. Still, there was more than one way to get there. Celestia may be able to block a teleportation spell, but she couldn't stop Nightmare Moon from flying there. She heard a noise in the distance, somepony was following her. She cast a dark shade to go investigate while she made her way to the castle.
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Nightmare Moon cursed loudly. Her shade had discovered that the lavender unicorn from the nearby town had gathered up a group of friends and were making their way towards the castle. She directed the shade to stop them, but every time, what should have been a fatal trap somehow ended up as a trivial encounter. She could detect the stench of Celestia's magic through the senses of the shade. Her sister was clearly intervening, saving the small group of ponies from destruction. Nightmare Moon was torn, she could go back and deal with the group herself, but she was at the castle now, and still had not found the Elements. The ruins were extensive and her inability to teleport was slowing down the search.
Nightmare Moon watched the group from a distance, the lavender one seemed to know where she was going. Perhaps Celestia had entrusted this mortal pony to retrieve the Elements. If so, all she had to do was wait and follow from a distance. The group slowly made it's way through the ruins, and entered a decrepit building.
"The Elements of Harmony, we've found them." she heard the lavender unicorn announce.
"Impossible!" Nightmare thought.
From high above, Nightmare Moon could see into the room they were standing on. It was empty. The two pegasus ponies flew towards the rooms center and appeared to grab something. The moment they touched the Elements the illusion spell faded. Nightmare Moon could clearly see the Elements resting on the alter in the center of the room. She spread her wings and dropped off the cloud she was observing from, flying towards the group.
The rest of the ponies left the room, leaving only the lavender unicorn and the Elements. Nightmare Moon sensed that with the Elements removed from the alter, the magic restricting her ability to teleport was starting to fail. She summoned a whirlwind to gather up the Elements and teleported, only to end up in another section of the ruins. It appeared that the ward against teleportation was not completely gone.
Nightmare looked around the room, the young unicorn was laying on the floor at the other side of the room. She must have jumped into the teleport.
"What a fool," she thought laughing manically.
#####
Twilight coughed, her lungs felt as if they were on fire. She looked upward and saw Nightmare Moon across the room, holding the Elements in her magic. Panicking, she did the only thing she could think of. With a stomp of her hooves and a snort, she charged the great alicorn.
To her complete surprise, Nightmare Moon dropped the elements and started charging at Twilight.
"Oh shit, oh shit, oh shit," Twilight thought. "What do I do?"
Twilight had one chance, she charged her horn and just before crashing into Nightmare Moon, she teleported over to the Elements. The pain was intense, her horn felt like it was going to explode, her lungs burnt and her whole body ached. She forced herself to stand and tried to give the spark of magic needed to set off the Elements.
"Come on!" she said, forcing more and more magic into her horn.
Nightmare Moon couldn't believe it, the pitiful mortal shouldn't have been able to elude her. Quickly she turned around and saw the pony standing over the Elements. They start to glow as the pony tried to bring them to life. She quickly teleported back across the room, only to arrive as the unicorn was thrown backwards. The Elements started to spark, small bits of magic jumped back and forth between them.
"No, no!" Nightmare moon said.
No mortal pony could wield the Elements alone!
Twilight watched, the sparking continued for a moment but then without warning, it died out. She gasped as Nightmare Moon started to laugh.
Nightmare Moon reared up and brought her hooves down, channeling a massive amount of magic into her attack. The Elements exploded into fragments. It was done.
"You little foal! Thinking you could defeat me? Now you will never see your princess, or your sun! The night will last forever!" she said, laughing at the cowering pony.
Twilight heard the sounds of her friends, approaching up the corridor behind her. It was at that moment the sixth Element revealed itself. Her eyes went wide and sparked with power. Her mind was filled with understanding as the Elements imparted their wisdom upon her.
"You think you can destroy The Elements of Harmony just like that? Well, you're wrong, because the spirits of The Elements of Harmony are right here!" she said.
The shards of the Elements rose from the ground.
As the unicorn continued to talk and the Elements reformed, Nightmare Moon looked on in shock. It was only through her and Celestia's great power that they had been able to wield the Elements in the past. No mortal pony should be able to wield them. Unless... could these mortal ponies have somehow be the living embodiment of the Elements themselves?
"You still don't have the sixth Element! The spark didn't work!" she said, not quite believing it herself.
"But it did! A different kind of spark," Twilight turned to her friends.
"I felt it the very moment I realized how happy I was to hear you, to see you, how much I cared about you. The spark ignited inside me when I realized that you all are my friends!"
She turned back to Nightmare Moon.
"You see Nightmare Moon, when those Elements are ignited by the... the spark that resides in the heart of us all, it creates the sixth element. The element of... magic!"
Twilight and her friends rose into the air. Nightmare Moon could feel raw power leaking from the ponies. She quickly cast her counterspell, hoping that it would be enough to protect her from the Elements.
A brilliant white light encompassed the ponies as the Elements came to life. They rose into the air, and a beam of pure Harmony surged forward and surrounded Nightmare Moon. Time slowed down, as she concentrated on defending herself. She poured more and more energy into the counterspell and for a split second it seemed as if her defenses would hold. Then she felt Celestia's power surge into the room.
Twilight's eyes flew open, glowing with godlike power as Celestia added her own magic into the spell.
Nightmare Moon realized she had been tricked. With the Elements of Harmony being wielded by the bearers, Celestia was free to add her own magic to the attack. There was no way Nightmare could combat both the Elements and Celestia at the same time. Celestia would imprison her for eternity. Her defenses failed and an intense pain overcame her.
"No! Noooo!" she said, screaming.
Nightmare Moon was immortal, eternal, she could not be ended. But she felt it, she was dying. It was completely impossible, but denying it didn't change the fact that it was happening. Celestia must have found a way to bypass Nightmare's immortality.
In a final act of desperation she relinquished control of the heavens, gathered what power she had left and focused it all on one thing.
Escape.
In a violent burst of magic, Nightmare Moon vanished from the room, a smoldering crater where she once stood was all that remained.