In a short story form...I just made most of this up. Enjoy!
Twilight took a deep breath. This was it. She was going to do it.
What was she going to do, you ask? Well as a matter of fact, Twilight had recently managed to rewrite Star Swirl the Bearded's temporary time travel spell, and altered it to where the magic would last as long as you wanted it to. Her mentor Princess Celestia had suggested she hold open court so everypony attending would see this magnificent new spell in action. Twilight had nervously agreed, and now, a week later, it was time.
The violet Alicorn tried to push down the anxiety twisting in her gut. What if she failed? What if the spell went wrong and ended up hurting her? What if she couldn't get back? What if--
"Are you ready Twilight?" A soothing voice asked. It was Princess Celestia. (Who, by the way, was at the front of the room standing next to her sister, Princess Luna)
"Um...I guess. I mean yes! Hehe..." She stuttered, slowly walking through the parting crowd to stand next to the sun princess.
"Cast it whenever you are ready Twilight. None of us knows if this spell will actually work, and it is alright if you fail." Celestia reassured with an almost warning glance. She knew all too well how Twilight could overreact from time to time.
Twilight gave an embarrassed grin before focusing her magic and letting it pulse through her. She had decided earlier to go back a thousand years ago and watch the whole scenario of Equestria's now much beloved Princess Luna going bad because she felt that no one loved the nighttime. Confused as to why her sister was neglecting her and treating her like a senseless filly now, and why her subjects seemed to think "Oh the sun is just so wonderful and radiant! And Princess Celestia is just so perfect! Let's play all day and admire her, but sleep through the far more beautiful night and not care about Princess Luna". It was quite tragic, really. And it was too much for the night princess to bear. She had let her dark side take over, literally altering her physical form and causing her to do things she would ultimately regret... A few moments later there was a bright flash and Twilight felt the ground disappear beneath her hooves.
A thousand years back into time later (Or so she thought), Twilight breathed a sigh of relief as she felt solid footing once again. She opened her eyes and was shocked to see the Ancient Ruin in the Everfree Forest right in front of her, with Princess Luna hovering above it. "Princess Luna! I don't understand--"
"Did you really expect me to sit idly by while they all basked in your precious light?"
"Precious light?" Oh! It must have worked! Luna's about to transform! I guess she chose to go to their childhood home to reveal her inner darkness. But wait...Where is Celestia? She's supposed to be here, right? Who else would Luna be talking to?
"There can only be one princess in Equestria! And that princess...Will be ME!"
Twilight looked around panicky, searching for Celestia. This doesn't make any sense. Maybe it's something wrong with the spell--
"There's nothing wrong with your spell Twilight. This is reality."
"What?!" Twilight looked up horrified, to see that darkness had enveloped around the night princess, and Equestria was witnessing its first ever solar eclipse.
(One dark transformation later...)
"B-but...why?! You have no reason to do this again!"
"Oh no? I get banished to the moon for a thousand years, then when I escape, I find my sister has let everyone forget and think I was an old ponies' tale. After you and your blasted friends tear my mind and flesh apart with the Elements of Harmony and purge all my power away, I meet a pretty little pink Alicorn who doesn't even rule anything but is still loved more than me. Then when the Crystal Empire returns and is granted to Cadance, Celestia still treats me like a foal and won't even let me go when I wanted to see that old place more than she could imagine! My presence would have inspired hope that the citizens would desperately need. After all, I saved them before with Celestia, and we could do it again. And every time Equestria is in a crisis, who does she turn to? Well?"
Twilight was unable to speak, still absolutely dumbfounded.
"YOU! You and your silly friends! She doesn't even tell me, an equal Alicorn and ruler of Equestria, until I notice it for myself. Maybe because I'll start crying and just get in the way. After all, I'm just her lowly baby sister who isn't special at all.
And if that wasn't enough, nothing has changed at all over one thousand years of torture, stuck in the place I once loved the most. In fact, it's worse! My subjects don't even see me as a ruler of Equestria anymore! They all think Celestia is just so wonderful and all-powerful and perfect, and she just accepts it! I'm just the other small Alicorn who never did anything special like saving Equestria from eternal chaos, or saving the Crystal Empire and everywhere else from becoming a dreary wasteland full of hatred and fear, not to mention sharp black crystals. All I do is play the part of that scary cannibal boogeyman who gobbles ponies' backsides on Nightmare Night. Well no more. I'm going to get the respect I deserve, no matter what it takes!"
And that's how Equestria was made!
Signing off, EpicLuna123