Well that I understand, but

I exist for one purpose
doesn't mean two purposes: To cycle the souls blah blah blah AND return everything to the zero world. He said one. I recall the Iifa Tree's "cataclysmic destruction of Gaia" being mentioned elsewhere in the game, so what I also don't get is why the Iifa Tree doesn't take Gaia with it.

I've been reading the plot analysis on GameFAQs, but the evidence supposedly presented throughout the game is all far too vague. The whole point of Sakaguchi's wish to "tell stories" should mean just that: We're supposed to be hearing/reading a story, not guessing one.

If the Iifa Tree theory is true then fair enough, but it means they've done a horrible job of telling the story: The idea that Necron was just some random dude out of nowhere was pretty much what we all saw when we in school (I was 16) finished the game for the first time and we panned the crap out of it for that reason. The evidence is there, but the evidence sucks and is too vague.

This does now answer my question though: Yes, apparently Necron is alluded to throughout the game, but they did a bad job of telling us.