The Sun rose. It rose amidst a brilliant glow of red and orange, a show of colours and lights that Princess Celestia was quite proud of. She had been raising the Sun for a long time, and her experience showed.
She watched the newly risen Sun for a moment, and then turned to the purple unicorn at the other side of her balcony tea-table.
“Now, Twilight. What is it that you wished to talk to me about?”
Twilight took a deep breath. This was going to be a difficult conversation. It would be better to get the biggest obstacle out of the way first, to place the least believable statement out there at once. She could then go into the reasoning behind it, the hundred little things that had told her precisely what was going on, which had led to this unbelievable conclusion. She braced herself for questions, for disbelief, for shock.
“Rainbow Dash is a changeling drone.” she said. She braced for the Princess' reaction, taking a sip of tea to steady her nerves.
“Yes, I know.” nodded Celestia. “Was that all?”
Twilight spat a mouthful of scalding-hot tea across the table. The teacup she had been holding with her magic fell to the table, wobbling slightly, and might have fallen had Celestia not extended her own field over the cup.
“HOW COULD YOU HAVE KNOWN THAT?” she yelled, jumping up and slamming both her front hooves onto the small table.
“All pegasi are changelings.” Celestia levitated a small tea-towel, cleaning up the tea that had managed to get itself all over the table. “The last true pegasus died some eight hundred years ago. I'd appreciate it if you didn't tell Luna, by the way; she's still trying to find some actual pegasi.”
“Eight – hundred – years?” squeaked Twilight, sitting down abruptly. “Wait... all pegasi? So Fluttershy -”
“Changeling queen.” replied Celestia promptly. “The animals that live in her house are almost all her drones. For that matter, so are most of the pets in Ponyville.”
“Including -”
“Yes, even Owlowicious.” nodded Celestia.
Twilight sank back into her seat, thinking of the implications. Another name intruded itself quickly upon her mind. “Cadence – I mean, Princess Mi Amora Cadenza – she – she used to be a pegasus before she was an alicorn, right? At least, that's what she told me... does that mean – is she -”
Celestia nodded. “Yes, Twilight. She is a changeling. There are – signs – that one can see. Ways to tell whether anypony is a changeling or not.”
“But – Queen Chrysalis -”
“I knew she was a changeling when I first laid eyes on her.” admits Celestia. “Where I failed, there, was in not realising which changeling she was – or, rather, which changeling she wasn't. She wasn't Princess Mi Amora Cadenza.”
“My brother married a changeling and you said nothing?”
“Your brother is a changeling, Twilight. I'm not sure yet whether each of them have realised what the other one is, but if they haven't, then they're sure to find out soon.”
“Wait, how is that possible?” asked Twilight. “Is he adopted?”
“No, Twilight. You are adopted.”
Twilight sat still in silence, staring at her mentor. “I'm... adopted? Wait, so my parents are...”
“Yes, Twilight. I thought that you might have got the first hint at your entrance exam, when they turned themselves into plants to try to hide when you hatched Spike and lost control. Unicorns are an endangered species. Almost extinct, in fact; to the best of my knowledge, there are only five true Unicorns left, and three of these are children, yet to undergo their final metamorphosis.”
“Final – metamorphosis? So, wait, adult unicorns – if there are two adult unicorns, then...”
Celestia nodded. “Luna and myself.” she said. “No adult unicorn stallions, which has been something of a problem for the last several centuries. Fortunately, recent advances in biology have resulted in the option of cloning – which is where the three of you came from, incidentally. Two female, one male, were all that survived to term. You and the other female were fostered out to Changeling families, under conditions of great secrecy. In order to recreate the unicorn race, incidentally, both of you will have to marry the one male after you come of age and have completed your final metamorphosis.” She sighed. “I had been hoping to wait awhile longer before telling you this.”
Twilight's mouth opened and closed several times, as all that she had believed about the world slowly crumbled around her.
“Earth ponies?” she asked, after awhile. “Surely earth ponies can't be extinct? I mean, Applejack -”
“Changeling.” said Celestia, promptly.
“...what, really? But... they've been living there ever since Ponyville was founded...”
“And did the name never strike you as odd?” asked Celestia. “Manticores don't live in Manticoreville. Griffon don't live in Griffonville. 'Ponyville' isn't the sort of name that ponies choose to name a town; it's the sort of name that's chosen by people who want everyone to think that they are ponies. The entire Apple clan is a Changeling hive.”
Twilight stared at the Princess, her eyes wide. “And... and Pinkie Pie? Surely she's not a changeling?”
“Oh, no, she's not a changeling.” said Celestia, taking another sip of tea. “By my count, she's at least fifteen separate changelings. Have you never noticed how, no matter how fast you run to escape her, she's always waiting wherever you want to hide?”
Twilight stared at her mentor for a long moment. She suddenly realised that her mouth was open, and shut it. “I... I always wondered how she did that... but... Earth ponies in general?”
“Extinct for at least four hundred years. As with the pegasi, if we can ever find a good source of viable earth pony DNA, we might be able to recover the species, though after so long...” Celestia watched her student carefully. Twilight, for her part, stared into space. An entire lifetime worth of assumptions were breaking down inside her head, rebuilding into a new worldview, being examined piece by piece.
The prior probability of Celestia telling an outright lie is low, no more than two percent. However, the prior probability that the world she is describing is true is also low. I should check first for inconsistencies in the provided narrative – ah, I think I have it.
“If almost everyone are changelings,” asked Twilight, speaking with the slow and careful deliberation of someone re-checking the question for consistency even as she speaks it, “then why continue to maintain this elaborate deception? Why pull the wool over everyone's eyes when they can just put us in cocoons and go back to their own shapes?”
“Oh, Twilight. Not all changelings are evil. More to the point, the changelings aren't aware of the extinction of the ponies. There are at least five thousand separate changeling hives trying to take over Equestria, and none of them know of more than one or two other hives. It's like a flock of wolves, all trying desperately to pretend that they're sheep.”
“Oh.” Twilight stared into her teacup for a long moment.
Time passed.
More time passed. Celestia finished the last of the tea in the teapot.
More time passed. Finally, Twilight looked up.
“So... there's five unicorns, and everyone else are changelings?”
“In short, yes.”
“And real unicorns go through a final metamorphosis, in which they grow wings?”
“Yes.”
“And Rarity and I will have to marry that other genuine male unicorn?”
Celestia raised an eyebrow. “What on Equestria made you think that Rarity was the other genuine unicorn?” she asked.
“But – but – she -” Twilight stumbled for the right words, and then gave up the explanation. “So... none of my friends are...”
“Well, I should hope that they're still your friends. Them being changelings shouldn't change who they are. But no, none of them are ponies.”
Twilight nodded, too shocked to raise an argument. “Then... who is...”
“I believe she calls herself the Great and Powerful Trixie.” said Celestia. “A true unicorn's magic is always somewhat stronger than a changeling's, which is why she had no trouble outdoing anyone who wasn't you.”
Twilight had one final question that she needed to ask before she went to find somewhere to sit, alone, for about six months and process all this new information properly. “And...the one male?”
“Prince Blueblood.”