The Episode III spoiler-filled reviews and impressions thread

[Weltall]

Well, she does speak to you directly a couple of times. But all the history that is provided to you in the game suggests that she was the puppeteer behind everything. And it basically explains to you when you find out abou the Ancients that she had the abilities to manipulate, to implant images into peoples minds, etc. I can't remember the exact quotes anymore, though.

Otherwise, it's all just one big coincidence that you find out that she was 'discovered', then immediately following everything bad starts happening in the world.

Oh, and certain portions in the game where she directly controls the characters gives it away, too. :p

Anyways, this is way off topic, so I'll drop it.

I'll break in to add that I believe that after Sephiroth reappears in the Shinra HQ, he is nothing more than Jenova's mouthpiece. His form is being used, and there is some of the real Sephiroth within, but it's really Jenova you're encountering and chasing the entire time.