Ha, wow, it's been a looong time since I've been on these boards....and an equally long time since I've touched a Pokemon game. I did play Sapphire, but it was "borrowed" about a week after I got it, so I don't really remember what went on in it. Now I have Emerald, and I'm actually doing okay on it...but now I'm kind of stuck:

I'm on the last gym in Sootopolis City, but the doors are locked...I have all the HM's except for Waterfall, and I defeated Team Magma and Aqua in their hideouts. Is there something I missed here? What do I have to do to get the gym doors to open?
Also, how do I get the Sky Pillar to open? I know I can get Rayquaza there, but it's the same deal with the gym; the doors won't open.

Thanks for the help.