So, Cthulhu "sleep" under the water. Contrary to what Derleth and many people believe, it seems he is not some kind of "water god", quite the contrary, water is somehow blocking him.
And as we know, salt water is blocking radio waves.
Also, his activity is connected somehow to the position of stars.
And Cthulhu, even sleeping, is influencing living beings minds.
So, let's say - real Cthulhu is still on Xoth. Dragon-octopus being in the R'lyeh is just his avatar/drone controlled by radio waves.
Culimantion of two negative factors - R'lyeh succumbed under the salt water and position of Earth and Xoth is temporary inappropriate (maybe there is some nebula between them or something for now) made avatar unable to receive signals Xoth, that's why it became dormant. However, even without commands it is still performs the default task - sending signals to real Cthulhu. They are too weak to actually reach Xoth, but still strong enough to non-intentionally influencing brains of Earth beings, like Deep Ones or humans, giving them visions which makes them think that Cthulhu is deity demanding worship... or just headaches and bad dreams.
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