It All Comes Clear In The End.
Twilight Sparkle has a secret.
A secret that has haunted her from the age of negative six and yes, that will make sense later.
For Twilight Sparkle is not truly a pony, she is something else, something more mysterious, something more mystifying, something that is... Some thing.
But we are getting ahead of ourselves, for our story takes place in the Canterlot Castle Throne Room, in Canterlot Castle, in Canterlot.
The Throne Room was quiet, it was so silent in fact, that had a pin been present, it would have been heard even if nopony had dropped it.
Twilight Sparkle had been summoned by Celestia to Canterlot on a matter of grave importance, though her letter divulged nothing of the details. Upon arriving, she was ushered into the Throne Room, where Celestia and Discord were waiting. After greeting Celestia solemnly, the Room quickly became silent, and over the course of ten minutes, with that same silence hanging in the air, it became quite uncomfortable.
Discord cleared his throat, and the silence breathed a sigh of relief as it was allowed to move on, "Perhaps I'm speaking out of turn Celestia, but shouldn't you explain why you've brought us all here?"
Celestia's eyes showed but a moment of panic, before her serene expression returned in, not force exactly, but something to that effect, "But Discord, I clearly remember that it was you who asked me to bring my most faithful student to this place."
"What?" Discord was not as smooth dealing with his own surprise, "Don't screw with me Celestia, I get enough of that from the nobles, I got your letter just yesterday, and it was made very clear that I should be here or you'd force me to attend another of your grating nephew's 'triangulation seminars'."
Celestias gaze hardened as she focused her eyes on Discord, "Now is not the time for games Discord, I was supposed to be spending a spa day with Lulu, but your letter said that this meeting was a matter of national security."
At this point, Discord started to chuckle, he started to laugh, he quickly stopped as Celestia's glare made it obvious he should explain what was so funny, "It seems to me, dear Celestia, that we've been duped."
"What?" it was Twilight Sparkle's turn to be confused, and also voice her confusion, "But who could fool two of the most powerful beings in Equestria?"
"That," replied a deep voice like rolling thunder, "would be me."
Twilight, Celestia, and Discord all quickly turned to look as the Throne Room doors were thrown open, revealing the owner of the magnificent voice.
"Tank?" once again it was Twilight Sparkle's turn to be confused, and rightly so, "Are you... talking?"
"Of course I'm talking, and I'm here to end the charade we've been putting on."
Twilight cringed, as terrible, horrible thoughts swirled in her head, did he know? After all this time, was it to be an apparently magical tortoise that revealed her secret? Of course, had she taken a moment to look behind her, then she would have seen similar looks of discomfort on the faces of the immortals behind her.
The air was tense, so tense that the tension was nearly palpable, of course everypony knew that palping air was a horrible idea, but it could almost have been done anyway.
As the tension in the air rose, and nopony broke the silense, sometortoise knew he would have to get the ball rolling.
"Very well," he intoned dramatically, "If none of you are ready to reveal your secrets, then I'll just have to go first!"
And with that simple proclamation, a golden light shone up from the tortoise's shell, momentarily blinding the other secret keepers in the room, and when the light settled, it was not a tortoise standing in front of them, but a pony.
"That hat!" Celestia exclaimed.
"That cloak!" Discord all but screamed.
"Those... bells!" Twilight spoke breathlessly.
"Yes, it is I," the brown-coated pony confirmed, his voice deepening further, "the legendary Starswirl the Bearded!"
Indeed, Tank had revealed his true form, but with this reveal would come another!
"I knew you hadn't died," Discord was somehow completely serious, "I even took up the power of chaos so I could find you one day."
"You don't mean?" Starswirl worriedly asked.
"I do!" And with that simple exclamation, Discord shone with blazing orange light, and when it cleared an orange mare with a red and orange mane stood in his place.
"Sunset Shimmer?" both Starswirl and Celestia spoke at once, equally surprised to see the mare in front of them.
"That's right, it's me, Sunset Shimmer, Celestia's former student, and Starswirl the Bearded's former lover!"
The servants outside the Throne Room gasped, but the beings inside were too important to notice them.
"It cannot be!" Celestia decreed, "You were once my student!"
"Yes Celestia, and it is with your teachings that I was able to find the power of chaos, the power to kill Starswirl!"
"But I thought you said you were lovers?" Twilight knew she needed to diffuse the situation before it got any more out of control.
"Once," it was Starswirl's turn to reveal some backstory, "but I told her from the beginning that I was never going to leave Luna for her!"
Once more the servants gasped, and once more they were ignored.
"It cannot be!" Celestia shouted, "You and my sister, were lovers?"
"But of course, and it was out of love that I spent over a thousand years honing my magic for this moment!"
Once again Starswirl was enveloped by golden light, but this time he emerged not simply as a Unicorn, but as a full-fledged Alicorn!
"But how?" Twilight queried, "I thought only Celestia and Luna, and Cadance apparently, could be Alicorns!"
"Then I suppose I had better come clean as well." all eyes turned to Celestia as she was enveloped by green fire, becoming a Changeling Queen with a white carapace and pink hair-like... stuff, "Behold! I am the original Changeling, Embryous!"
"It can't be!" this time it was everyone's turn to be surprised, even me!
"But how could you lie to me for all these years?" Twilight Sparkle felt betrayed by her mentor, now revealed to be Embryous.
"Because Twilight," despite her nature, Embryous' voice was caring, "I have known of your own secret since the beginning, and the time has come to reveal your true form!"
In that instance Twilight Sparkle knew true joy, finally she would be accepted for who she truly was.
The transformation took but an instant, it was not a flashy lightshow, nor was it lit with gaudy fire, but there before everypony's eyes, was Twilight Sparkle, Draconequus!
The servants fainted, but they were ignored, as the four powerful beings in the room were far too important and fully revealed to pay attention.
"No!" Sunset Shimmer was afraid, if either Twilight or Embryous sided with Starswirl, she was doomed, "Celestia, please tell me you want vengeance on the man who took your sister's purity!"
"No Sunset," Embryous smiled serenely, the truth finally becoming clear, "I think Starswirl is the perfect stallion for my dear daughter."
"Daughter?" in that moment Sunset Shimmer knew she was boned.
"That's right, and I don't take kindly to any mare who tries to kill my future son-in-law!"
At her words, she, Starswirl the Alicorn, and Twilight the Draconequus descended upon the bitter mare, vanquishing her for all time.
"So you're not hung up on the fact that I cheated on your daughter?"
"You understood that it was a mistake, and your love was strong enough to spend over a thousand years as a tortoise to be with her, so I'll forgive you just this once."
"And what about me, Cele- uh, Embryous?" Twilight Sparkle floated uncertainly in front of Celestia, unsure of what to say.
Embryous smiled, she knew that a long hard week was ahead of her, but it would be the most fulfilling week of her life.
The coming weeks were the strangest Equestria had ever faced, with half the population revealing themselves to be Changelings, the most pervasive headline was that Blueblood wasn't one.
Strangely the return of Starswirl the Bearded, his attainment of Alicorn status, and his betrothal to Princess Luna was overshadowed by Luna's own revelation that she was a magical construct, not a Changeling. Of course Chrysalis told any tabloid who would print the news her sob story about how Luna was always 'mother's favourite', but mostly everyone found her whiny.
Twilight Sparkle was unsurprisingly accepted back in Ponyville, though it helped that Embryous kept the truth about Twilight a secret until after the populace found out about Scootaloo's father being a chicken, Mr. Cake secretly being a unicorn with a high-riding horn, and Fluttershy being a closet carnivore.
After all that, a Draconequus seemed almost normal.
But in the end Equestria returned to normal, Fluttershy was given counseling, Twilight returned to the library, and Spike confessed his true feelings for...
Big MacIntosh?