I believe I have finally found a way to make a half-decent story in which I can reconcile and explain away the silly and ridiculous control that ponies have over the sky and nature, and have that actually play a role in the theme of the story. I didn't mean for that to happen when I started typing this idea out, but whatever. I'm pleased with it.

Ezn and Short Skirts & Explosions, this one is for you. Hooray for making mountains out of molehills!

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Twilight Sparkle had always possessed a rare neurological abnormality - one which made her capable of great power. However, what makes it dangerous is that it is unleashed at random periods during moments of intense stress, shock or uncertainty in life. It came loose when her stress grew beyond dangerous levels in Lesson Zero (and she performed that very advanced mind-altering spell on par with Discord's trickery as if it were no big deal), it happened when she lost her patience with Pinkie Pie's illogical claims (and her mane turned to fire), and it happened during her entrance exam, when, after the most stressful performance she ever wasn't prepared for, the unexpected shockwave pushed her past that threshold for the first time.

Celestia saw the baby dragon grown to great proportions, and immediately knew from experiences eons ago that Twilight was the latest afflicted unicorn in the world with this disorder (being one so young, and capable of such sudden power). She had taken Twilight under her wing to keep her safe from herself, and her other subjects safe from future outbursts, but also in hopes that this "affliction" could be harnessed. Her decision to send Twilight to Ponyville had been a dangerous gambit, wherein the possible outcomes she had pondered included Twilight defeating Nightmare Moon on her own, or the triggering of a rare metaphysical chain reaction that would cause a colossal implosion, vanquish Nightmare Moon once and for all but annihilating a large swath of land and leaving an enormous bowl-shaped crater. However, these were the worst-case scenarios she had considered, and most importantly, she sent her to Ponyville and assigned her to friend-making because the subset of magic conjured through friendship had both the best chances of vanquishing Nightmare Moon, but moreso of bringing healing and stability to her volatile student, who she loved. It was also in her long-term interests: her ultimate goal, to tame that power. She desired to eventually control the outer sky.

(a bit of background / world building) By their virtue, these polychrome equine races control, manipulate and govern their environment entirely, whether consciously or unconsciously; the elements are sympathetic to their actions. The age of ice that lead them to discover Equestria was an example of their involuntarily stalling warmth by failing at reconciliation. However, this aura of control extends only as far as the they inhabit the world. Pioneers and recluses who had traveled and lived beyond the farthest borders of Equestria have testified that  the plants grow on their own, the animals take care of themselves, and the weather governs itself. However, most significantly, there were rumors that during the Nightmare Moon incident, the sun rose and set naturally - both the first one and the second one. Furthermore, Discord's abuse of nature only ever extended as far as ponies (whose hearts, and thus nature around them, could be corrupted).

The prospect of nature (and moreover, the sky) not under the benevolent governance of ponydom had always troubled Celestia, and been a point on which Chrysalis had taunted her (in that, though she was a changeling, she lived outside of the pony illusion). By fiat of good-is-what-I-agree-with, and how life for ponies was always safer inside of Equestria, the princesses had kept the wool over ponies' eyes for eons, having convinced them that their own magically-contrived nature was the one true nature, and existence outside a lie.

(and now, the actual story)

One night, Twilight Sparkle has a dream that, during a bright and peaceful day, the sky shatters as her brother's spell around Canterlot had, exposing a night that Celestia and Luna were powerless to change. A horde of changelings from beyond the eggshell sky invades. In her dream, feeling her world crumbling, she surrenders to the inward pressure of the cold and unsympathetic universe that the changelings had exposed. In the anger and anguish of her nightmare, she involuntarily conjures the implosive chain reaction spell, which not only draws in the changelings, but also implodes the world and and draws the true stars down to her, snuffing out all of existence, including herself. When she wakes up from that nightmare in the middle of the night, every book in her library is piled on top of her, and she can barely breathe. Spike had just sent a letter to the princesses, and is frantically digging through the books to pull her out lest she suffocate from the weight of books that had assailed her in her sleep.

Luna, knowing some of what her sister had told her about Twilight, put her governance of the night on hold to console her, offer her counsel, and to ask questions about the dream; the involuntary magic was a warning sign of the affliction destabilizing. However, Luna unwittingly revealed that beyond merely being skillful and gifted, there was another reason for the personal tutelage. Twilight suppresses her surprise until after Luna leaves the library. She launches immediately into studying and searching for answers, beginning with the pile of books that had collected around her, trying to find out what is wrong with her, and what about her dream could be so noteworthy (apart from it being mirrored in reality). Celestia reprimands Luna for the slip-up, and reveals to her sister the full extent of what Twilight is.

Over the next few days, Twilight begins a soulsearch wherein she meditates and studies herself, and tries to purify herself of every trace of malice that might exist; knowing half of Celestia's motives, she fears that she might be dangerous to Equestria. She implores her friends to tell her all of what they perceived as her faults, and slips into occasional bouts of self-loathing as traces of the nightmare wherein she  destroyed the universe return to her. Her friends assure her that they love her and that they know her to be a kindhearted individual. However, she begins to doubt the very concept of friendship; her friends could not see the evil that she discovered within herself. Spike worries about her and wants to stay by her side the whole time, but Twilight argues to him (and the rest of her friends) that she might be a danger to him and all else around her. She makes the point that she will be finding her true self, and that once she sorts everything out, she'll be fine. Celestia tasks Spike with surreptitiously following Twilight into the library for the rest of the week, fearful that a direct confrontation with her, in light of her discovery, might only worsen matters. Rather, she carefully discusses how to approach Twilight with her sister, using Spike's updates to strategize and carefully plan their words.

Twilight then one day finds, deep in a restricted section, a historical record of a unicorn whose mental afflictions were uncannily similar to her own. She then changes her search into one for a solution, studying recursive cognition and the alchemy of consciousness (for self-study), learning tricks and mental enhancements spells that accelerate her hunt through the Equestrian archives for a cure (or the key into the deepest part of her mind that might contain the untouchable knot in her soul). A few days later, she acquires the skill of reading books remotely, which aren't even open, and achieves a remote awareness of written and spoken words, to be able to further accelerate the exponential growth of her mind. On that morning, Celestia and Luna approach the archives and are discussing her. She sits in silence and listens, deducing and inferring every secret from their words.

They enter, and Twilight confronts them, especially Celestia, on the matter of having kept secrets from her (and her parents, who hadn't been informed of the grand experiment). Celestia and Luna are unable to retort, but merely agree. The last vestiges of her world and the understanding of the relationship between her and Celestia are then shattered. Vindicated but emptied, Twilight's mind then turns a decision: shatter the sky herself, rather than wait for Equestria's enemies do so, in order to thwart the prophecy of her dream. By teleportation she abruptly slips away from Celestia and Luna and to the temple of the sun and moon where the elements of harmony had once stood. Twilight then sits before the orrery in the temple and begins to meditate, trying to willingly summon the power within her and use it in a controlled manner to draw down the contrived sky of ponydom, using the insincerity of Celestia as the key to unlocking herself.

Meanwhile, Celestia finally comes to terms with her folly and naïvety regarding Twilight, and just wants to have her back as a beloved student. She declares a state of emergency throughout Equestria, knowing Twilight might cause very grave damage if she destabilized. She brings the elements of harmony, and their bearers, together, but without the crucial sixth element. Elite scouts are sent from their outposts to search for Twilight throughout Equestria, but then, at sundown, a brilliant column of violet energy from the temple of sun and moon stabs into the sky from the temple. The royal sisters and the element-bearers try to approach, but it's too late. Having opened the floodgates of the great reserves of power within her existence, she had poured her magic into the false sky. Before the sun can set fully, she tears the false sky asunder and gazes into the hearts of Equestrian citizens from an elevated state of awareness. She whispers to them all, reassuring them that she means no harm but merely to reveal the true sky, which like her, none shall ever control. She becomes disappointed when all of ponydom responds with joy turning to fear, and security to uncertainty and helplessness, despite all of her reassuring whispers from the sky. Feeling betrayal and scorn, Twilight begins to despise ponydom; they deceive themselves with their saccharine false reality and cannot coexist with the universe's true reality.

However, Celestia, Luna, Spike and her five closest friends are impervious to her gaze. It is the chord of familiarity that introduces the doubt that she fully knows them, given how she had thought she had known them in the past, before her awakening, but also the fear that probing into their minds would violate a sacred and ineffable trust that she nonetheless wanted to violate in order to be certain of who they truly were. They stand before her transfigured body in the temple, imploring and interceding on behalf of ponykind. Not being able to use her extrasensory perception, she enters deliberation with them, probing them with her words. It is at this point revealed that all of Twilight's friends had been made aware of her affliction, as of the events in Lesson Zero. She is furious with them, and questions them on how they could bear with her and truly love her, when that love could just be concern that the passion and anger within her posed an existential threat. She thus questions them on the matter of trust: of how, by exercising caution and tact around her, cushioning her from their awareness of her (and what she was), they could possibly remain sincere.

Finally, Spike speaks up and reminds her of the times when she hypocritically fretted too much over controlling her circumstances. He cites them to point out that he didn't want her to hurt herself (and neither did her friends) because they were worried for her safety. Rainbow Dash speaks up and explains her perspective: as an athlete, putting things out of her mind while performing is essential to performing, and how all her friends wanted her to be happy until they could find a cure for her. Rarity speaks up and tells her that they only wanted the best for her, and had the best of intentions. Pinkie Pie backs this up by reminding her of her birthday, when she thought everyone had been lying to her. Finally, Applejack solemnly declares, in a sudden flash of insight that belies her element: as important as the truth is, declaring truths and non-truths concerning what is in your head is neither possible nor safe, because you can actually influence your own self through such declarations to begin with. Celestia substantiates this with the statement that they did not fully understand her or her affliction yet; thousands of years of research had not yielded an explanation or resolution to Twilight's affliction. Her friends hadn't told her about herself because by the very act of stating things about her, they might influence her.

At this pronouncement, Twilight awakens to the folly and illusion of awareness and control over herself, likening it to the same control that ponykind had exercised over its environment. With far less wrath than moments earlier, she asks Fluttershy what she has to say for herself and her friends. She says that even though they don't fully understand her, and that she doesn't fully understand them, she tries to put that out of her mind. She instead strives for mere kindness, because kindness empty of all rationale and motivation is the only truth and the only constant on which she relies; it is forever beyond reproach. Upon hearing this, Twilight releases her spirit from the sky and reenters her body in full. She then falls from playing god to flowing tears, and her affliction leaves her soul in the form of a brilliant white comet that skyrockets into the cosmos. With tears of reconciliation, they all embrace beneath the first true night sky that ponykind had seen since its very conception.