//------------------------------//
// Why? 
// Story: Discovery of the hidden dragons 
// by EveryAlternateEnding 
//------------------------------//

Celestia was relaxed. Her foreign affairs tour had had a few bumps in the road (one misspeak could offend a yak to no end), but all in all, Equestria's relations with other nations were improving. Her last stop was Civil Dragon Commune, a place in which Celestia expected no issue. Spike, the foreign ambassador, welcomed her in. His elderly wife, Fluttershy, stood next to him, the only pony in the village.

The town was now fifty years old, and had grown from being seven dragons come down from the Dragonlands to live as ponies to being nearly one thousand. There were vast fields, a gem mine, a large, fenced-in herd of caribou, and a fair amount of domestic animals that the dragons had bought from ponies. There was a school, a town hall, and meeting circle that would be their meeting place that night. A feast was held beforehand, in a storage silo turned dining hall. It allowed Celestia to chat with Smoulder, the first dragon student at Twilight's School of Friendship and one of the founding members of the commune. In a while, the non-officials would clear out and the meeting would begin: a simple matter of renewing the trade contracts and international legal documents that were about to expire. That wouldn't take more than an hour, and then she could go home at last.

From Canterlot castle, Twilight was using her magic to watch. She knew she shouldn't be, but, well, she knew where Celestia would be and wanted the reassurance that Celestia was still the good, kind pony she knew.

Why would Celestia do this? Did she order the experimentation, or was it someone else? There was only one thing to do: wait and ask.

At nearly midnight, Celestia teleported herself from the commune to her chambers, only to find herself nose to nose with Twilight Sparkle.

"Celestia, I need to talk to you." 

"Why the grim face, Twilight?"

"I found the dragons. Tell me about them." Celestia looked puzzled. Twilight's tone hardened. "The ones in the barn. The ones that experiments were done on."

Celestia's mouth hung agape. She never thought this could happen. Until Twilight mentioned the barn, she hadn't even considered it. "Twilight, please stay calm! I promise you that it's far more reasonable than you think. We'll have a civil discussion, and then we'll talk about solutions."

"Solutions?! They've-" Twilight started, yelling. But then she calmed down. "Alright. Let's hear it. What's going on?"

Celestia sighed. "Twilight, when were you born?"

"A decade or two before the return of Luna. Why?"

"Because that means that you're old enough to remember back when we thought dragons were no more sapient than a dog. Don't you remember all that hullabaloo that happened when Spike spoke for the first time? We had no idea that was possible!"

"I do remember that!" Twilight said, almost laughing. "You guys had had him registered as a pet lizard!"

"Yes. But anyhow, the migratory dragons hadn't reached Equestria. They'd left during the reign of Discord and been gone a thousand years. And Twilight, after the reign of Discord, many things had changed. Many recombinant creatures such as manticores and the cockatrice were made by him, for instance. So when the sapient dragons left, leaving behind only the feral ones who had lost their minds to greed, we thought that that was just how they were now. They were monsters that I had to protect my little ponies from. I eventually came up with the idea to capture their eggs to prevent them from overpopulating. We didn't know that the dragons we were dealing with were hardly in any position to look after hatchlings. And after that, it was a short step to using them for teaching purposes and research. Research especially, as it could be used to learn about the dragons so we could better defend ourselves against them. Then, you, my protégé, hatched Spike's egg. You nearly cried when we tried taking the hatchling away for research, and so I decided, well, why not? Let her keep it. They're tiny, wingless, and relatively harmless for the first fourteen or so years of their lives. I wouldn't have done it if it weren't for the fact that you'd be so close to me. A few years passed, and it became more and more apparent that he was sapient. I knew then that I'd made a horrible mistake, especially since it seemed that a group of dragons were going to be migrating here within a few years. I rented some trucks and had the researchers quietly pack the young dragons in, blinded and muzzled. I led them into the stable and tended to their wounds. I took the hoods off for that so that they'd see me as a friend and not a foe. And Twilight, let me tell you, I was terrified to take off their restraints. Some of them were somewhat violent. I've kept them in the barn ever since. I alone see them. I had the researchers assigned the to new tasks immediately and never told a soul why the project had been shut down, just that there had been violations. And that's the whole story."

Twilight was silent a long time. "Well, I'm glad it was nothing malicious. But Princess, why keep them in a barn?"

"What else could I do?"

"You're telling them all kinds of weird things. Like to cut their webbings-"

"So they're less dangerous. So they don't fly away."

"Then what about their height? Some of them are so short that they haven't even hit puberty point."

"Dragons grow by owning things. There's a lot of them. I couldn't bring in enough things for them to all grow without attracting attention. And what would the benefit of them growing bigger be, to them or anyone else? They don't have to hunt or protect themselves against anything."

Twilight fell silent: a silence that lasted over half a minute. She had come into this situation fully believing that her mentor was terribly in the wrong. Now she didn't have a clue. "And why is is that? Why don't you let them go?"

"Where would I put them that benefits me, them or anyone more than the current arrangement?"

"As far as you knew when Spike had just begun to speak, dragons lived as wild animals. Why not just release them?"

"For what? We didn't know how much of what dragons need to know to survive is ingrained and how much is learned. I could have been sending them to their deaths. And if I wasn't, we'd have hundreds of extra predators in Equestria. It just wouldn't be to anyone's benefit."

"...I get what you're saying. I really do. But it still seems wrong."

"I know. I'm Sorry. But it's unchangeable now."

Twilight nodded. She knew that Celestia was right. Now that dragons and ponies had their allegiance- and not a particularly stable one, at the moment- this history of racism and abuse could break it. The Dragonlands were already somewhat suspicious of ponies destroying their lifestyle thanks to the Civil Dragon Commune. The barn had to stay hidden for the sake of peace. "I won't tell anyone." Twilight said with resolve.