Okay so there was a whole ton of shit going on in RS arc and there was some stuff with rayquaza sure.

We know this is the role that Rayquaza played in the RS arc, as well as the games obviously.



And he was woken up by Wally.  It was Wally's Big Hero Moment in the RS arc!



Norman rides Rayquaza into the fray, but suffers greatly because he has no medium (a jeweled orb) to control Rayquaza with.



And Norman ended up dying because of it.  (How he survived/what was different in the Celebi-selected timeline, I have no idea.)  But this informs us that Rayquaza was being held for research, in order to create the gem that would control it.  If you look, you can see that the gem inside is the same thing that Emerald sticks to his forehead.  (Which is incredibly stupid even by pokespe standards.)


And then the more detailed flashback of Rayquaza's escape:





Okay are you ready for the really cool part



If the part with the association's motivations is ever explained I can't find it.  We know they were making a jewel for rayquaza, but why, exactly?  There doesn't seem to be an actual explanation as far as I can tell.



There is an item in the recent games for Rayquaza, however!

You get this sucker from Professor Oak in HeartGold/SoulSilver, after bringing him both Groudon and Kyogre.