The Old Gods like to be cryptic. Until whatever these things refer to (at least the less obvious ones) are revealed speculation and theory are all we have, so it's anyone's guess what it all actually means.
Il'gynoth is a "manifestation of the horrors that lie at the heart of the Nightmare", meaning it's a part of N'zoth. Same deal as with Xal'atath (although we don't know which Old God it came from).The thing is though, it says "we" throughout the fight from start to near finish, except at the end where it says "I". What is Il'gynoth actually?
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.....Neat.