Elder storyline?

So, did I get this right? I have to fight the shaper to make sure that the elder gets strong enough to occupy maps on the atlas. Once he is strong enough I smack him with the help of the shaper. Maybe I missed some elements of the storyline but this does not really make a lot of sense to me. Help!

Hentai tentacle monster that wants to do naughty things to shaper.

But why do I have to smack the shaper first? Wouldn't it make more sense to just fight the evil cthulu guy immediately??? I am confused.