(Unfortunately, scrounging up this image's source spoiled me on suspicions of Airy. The artist's Facebook said he'd played into the late chapters, and "then THAT happened." Further, tried to copy+paste the deviantART URL, and saw the image's title that way. I'm only as far as the engine room boss fight, and while I've picked up suspicious vibes from Airy, now I'm full spoiled that something is going down poorly with her. Ah, if only I could lance my brain, or quarantee memories, that I may have seen this play out as intended. Damn you, Internet!)

To be fair, you will pretty much know what's going on very soon, and for most of the game. It's just set up in such a way that by the time you find out you're kindof powerless to do anything about it. You could almost say you're hostage to whats going on.

I never thought I'd say this, but at least Kyubey is not as evil as Airy is. His methods may be incredibly fucked up, but Kyubey does what he does to preserve the universe. Airy just seeks to bring ruin and have Ouroboros rule over what's left.

"Very soon"? That depends on the person. Unless there's telltale hints of her true nature that I missed earlier, it only starts to become somewhat apparent after the second time all crystals are awakened. I accidentally spoiled myself by destroying a crystal in Chapter 4 or 5 when I didn't expect it to (I thought it would lead to a Game Over), so her true nature came as a complete shock to me.