Twilight sat in the centre of a large room, surrounded on all sides by massive bookcases stretching as high as the eye could see and packed full of books, scrolls and tomes of all shapes and sizes. He was reclining in a nice (and rather expensive looking) chair set on a beautiful, intricate carpet and sipping at tea while sorting through dozens of scrolls. All in all it was exactly the kind of place that normally would have had Twilight bouncing in anticipation of potentially lost knowledge.

But as it were, it was not actually a place (well not by the most literal definitions of the word) but rather a metaphorical representation of a highly abstract concept, the innermost sanctum of Twilight's mind.

Twilight had originally built the place at a young age (perhaps at the youngest age anypony had ever built such a mental construct) as a place where she could retreat so that no bully could hurt her. Naturally, her mental control as a child was limited and the 'mind library' had been in constant flux. As Twilight grew in both age and control she had discovered additional uses for the library as a memory aid (contrary to popular belief Twilight did not actually have a photographic memory) and as a place to collect her thoughts of the past day (spending one hour sorting new memories made the remaining night on average thirty-five percent more restful and ninety percent less likely to spawn a nightmare).

And, right now sorting of recent events was desperately needed for the royal mare-turned-stallion.

The lavender alicorn sorted through the scrolls and papers floating around him, each one representing a fact or event from his waking hours. 'I am a stallion now', 'I am no longer a mare', 'I will be a stallion for the rest of my life' and 'I will never be a mare again' were all amongst the most prominent and important of the facts (redundancy never harmed anypony (except when the item of redundancy was intended to harm somepony (or when the redundancy distracted from an important thing intended to harm somepony (or when redundancy resulted in the abuse of parentheses causing readers to repetitively hit their heads against a wall (but that would never happen)))))

Twilight was having trouble completely accepting what had happened to him. He knew empirically exactly what he was now: male, colt, stallion, masculine, a mix of X and Y chromosomes rather than just X, but his subconscious was having trouble accepting the truth. It was like the deepest parts of his mind were still in denial (which was not surprising when you consider how traumatic an event as permanently changing one's sex is upon one's sense of self) and the whole issue was complicated furthermore by Celestia's letter. Twilight knew the eldest princess well enough to know that the letter meant much more than what it said, but he didn't know her well enough to know what it meant. It was sad, really, that, even with the many years Twilight spent with Celestia, Twilight had never gotten to truly know the princess (although not without trying, but every time Twilight had asked about the solar alicorn she had been met with many thousands of years worth of expertise at conversational manipulation).

Hay Twilight probably knew Luna better than Celestia, and the amount of time she had spent with the lunar princess was a mere fraction of the time she had spent with her elder sister.

Luna! The thought burst suddenly into his mind who would know Celestia better than her own sister.

Twilight decided that he would need to talk to Luna as soon as possible, and he was not comfortable revealing his change to the public yet

But Twilight would not need to go out in order to talk with Luna. After all, she was not called the 'Matron of Dreams' for nothing, and while a mental construct is not technically a dream, the difference was mostly theoretical. All Twilight would have to do is use a simple beacon spell and aim it into the Dream Realm, where Luna would most likely be watching over the dreams of the ponies of Equestria.

Luna was bored. She flew through the black void that composed the background of what was commonly called the Dream Realm; passing the little balls of light that represented the dreams of ponies (if another were to enter this realm they would be struck with how it was almost like flying among the stars in the night sky), and searching for even the smallest sign of distress. But it was to no avail; it seemed like everypony was sleeping soundly with happy dreams tonight (the closest thing to a nightmare that Luna had encountered so far was a mare dreaming about turnips, but right before Luna had intervened out of sheer boredom, she remembered she loved turnips rather than hated them). Luna would have even preferred to do her weekly night court (it had originally been nightly, but had been changed to weekly when nearly nopony showed up) over this. At least there was something to do during night court; even if it was listening to spoiled brats of nobles whine about something or other.

As Luna passed another dream she felt a burst of magic pulling her towards a particular point that seemed somehow more distant. Having nothing better to do the lunar princess allowed herself to be drawn in. As she drew near she could feel herself leaving the collective unconsciousness of ponies' dreams and entering this odd dream.

Suddenly, with an almost audible snap Luna felt her connection with the dream world snap and colour erupted around her with such intensity that her vision was blurred. Even with her sight impaired as such she could feel that this dream felt significantly more solid than most.

As Luna's vision cleared a familiar lavender shape coalesced in front of her.

“Twilight?”

“Yes it's me; I'm sorry about bothering you Luna but I really needed to talk to you” The lavender princess said in a comforting baritone.

What?! As Luna's vision refined further she noticed more than a few things off about the other alicorn, she had sharper and more defined features, smaller eyes, broader and taller shoulders, more pronounced muscular definition. I was almost like the younger alicorn had changed ... into a stallion. Luna's eyes widened as she realized what had happened, and proceeded to do the only thing that made sense in the situation.

“Twilight, we swear unto the Styx that 'twas not our actions that caused this strife to befall thee”

“What?!”

“Um, 'tis not our fault that thou wear the face of a stallion?” the statement sounded more like a question than anything else.

“I know what you mean,” Twilight's eyes narrowed “but why would I suspect you?”

“Did sister never recount that story to thee?”

“What story?”

“Well, we may have done to our sister something similar to what happened to thee”

“You turned Celestia into a stallion?!” Twilight was shocked

“Um ... yes?”

“What happened”

“Well she adapted much better than we had anticipated and if not for the nature of temporary transformations, we'd wager near all of Equestria would be able to trace their lineage directly back to her; if thou knowest what we mean.”

“Ugh, I did not need to know that.” Twilight scowled, before his face fell into a resigned expression “So the spell was temporary?”

“Aye, 'twas a temporary spell lasting but a year.” Luna thought for a second “Art thou implying your change is not?”

“Yes, whatever caused my change is not temporary; it was the first thing I checked.” Twilight sighed

“Thou know not of what caused the change?”

“No I haven't the faintest clue. I was using a spell written by Starswirl designed to balance magic and clean the ley lines of the body when 'boom' the spell backfired, and when I awoke I was as you see me now.”

“Hm ... we cannot help thee, if you wish to change back. Thou must understand that, in a distant time, such spells nearly caused disaster.”

“I know, Celestia already gave me the history lesson, but that is not what I called you here for”

“Where is here exactly, 'tis much too solid for a dream”

“It is the physical representation of my mind, a mental construct solidified. I learnt how to build it from a tome on dream arts by a mare called Soul Song”

“Our student Soul Song? We thought our sister had destroyed all her work because 'twas too dangerous”

“Trying to get a Twilight to destroy a book is like trying to make a parasprite stop eating, it doesn't work very well. Even more so when it's an ancient book detailing a unique form of magic.”

Luna had heard of the incident involving the parasprites “That ... is an interesting metaphor young Twilight”

“Simile. I used to say it was like reforming Discord but then Fluttershy went and did it, and after he ate all my reformation spells.”

“Reformation spells? As in mind manipulation spells?” Luna asked worriedly.

“Oh, not at all. They were just designed to give large and painful electric shocks whenever he does something bad”

The lunar princess's eyes widened in shock. Sounds a little too much like a curse, We are not surprised he did not want that used upon him. “Yes, we understand. What was it for that thou called us here tonight?”

“Well, after searching my entire library for a counter-spell, I decided to send a letter to Celestia asking if she could help” Twilight's horn ignited and a scroll floated over to Luna “And this is what she sent back”

“'Tis not our sister's hoofwriting”

“No, it isn't. I do not have a photographic memory, and the original was destroyed, but these were her exact words”

Luna read the letter through. “'tis definitely Celestia. Our sister, like everypony, has a certain” Luna paused “way in which she speaks and writes that could not be falsified”

“You mean that you could tell if the letter was authentic just by the words that were used”

“No, not the words, but rather what lay behind, a kind of essence of the one writing or speaking. 'Tis very abstract.”

Twilight had a very skeptical look on his face “How very poetic of you Luna”

“We do not expect thou to understand, our sister never has, and most likely never will. As for the letter, we see nothing of an insidious nature. However, we have been away for quite a time and are no longer as close to our sister as we once were”

“What about the last line?”

“To tell thee the truth, we are not entirely sure. Although we think it may have been a statement from her own experience as a stallion. Or it may have been a statement trying to put thee at ease” Luna frowned, “And if anything, our sister is understating how near we came to disaster. If we remember correctly Equestria went nearly sixty years without a single colt birth.”

“Nearly sixty years, without any colts? How did ponykind survive?”

“'If they are not born, they must be made.'” Luna quoted an old “acquaintance”.

“Made? Do you mean that fillies were transformed into colts?”

“Aye,” Luna made a very sad face, “And doth thou recall The Third Law of Transfiguration.”

“'To undo is many times more difficult than to do; as to undo you must not only reverse the original transformation, you must do so while fighting the original magic' It's why nearly every transfiguration spell has an innate time limit built into the spell.” Twilight's eyes widened, “But with the hereditary lingering of many, many permanent spells, and since this was before the push to standardize spellcraft they would all be causing the same effects through many slightly differing means, combined with how chaotically spells tend to interact and magic's innate capability to take on a life of it's own ... to do such a thing would have been very difficult indeed.”

“Indeed, 'twas very difficult, in many different ways. With most of the greatest mages of the time working on the solution, we just barely succeeded. And the equine cost ... it still lays heavy on ourself and our sister.”

“The 'equine cost'? Do you mean ...”

“Yes.” Luna shed a tear, “Our counterspell was barely worthy of the term. Many, too many, of our little ponies didn't make it. And even more lost their lives in the pursuit of that goal.”

Twilight looked shocked,“That's horrible.”

“'Twas a very dark time in Equestria's history, but failure, extinction, was not an option.”

“I think I can understand why Celestia is so adamant about this. I'm still frustrated, but I understand.”

“That is all we can expect.”

“Thank you Luna, you were a great help.”

“No, we thank you young prince. 'Twas a very dull night before thou called us here. But we must not take anymore of thy time, thou must retire to thy dreams”

Luna felt herself leave Twilight's mind. She looked to her night sky above where she lay. Tonight was not as dull as we thought. And young Twilight makes quite the stallion. Luna blushed, not certain where that last thought had come from.

Here is the updated chapter 2, I significantly edited Luna and Twilight's conversation, the old version was based on the original chapter 1 where Celestia didn't explain why Twilight couldn't turn back and Luna barely even expanded on it. I hope I have made a it believable why transforming back is so illegal.