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If I remember correctly, she doesn't die yet.
Spoilers
About the temple, it's been a long time, but I think you get the Black Materia, the temple dissapears/disentigrates/crumbles, something like that, and all that's left is a fairly small pit. Sephiroth appears and forces Cloud to take the Black Materia from Aeris and give it to him. Sephiroth dissapears with it, and Cloud can't remember what happened.
More spoilers
Apart from that, I know Aeris leaves sometime around there or later, and you end up going far north, to an ancient ruined city, and eventually find Aeris, then she gets killed. You already know who kills her. Also, remember that "Jenova" thing from the boat ride? It's back.
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