This song is (pretty much obviously) about R'lyeh, the Lovecraftian underwater city where the Elder God Cthulhu "waits dreaming". This city is described by the author as devoid of any human logic and provoking a viewer's insanity by defying ratio and Euclidean geometry.
From the perspective of a cultist - a worshiper of Cthulhu, enthralled and fascinated by him/it - this song praises the terrifying and mighty nature of R'lyeh, barely mentioning its long asleep inhabitant. But it still alludes to the Rise of Cthulhu, and altogether of the city, as it is a recurrent pattern in Lovecraft's writings: “Who knows the end? What has risen may sink, and what has sunk may rise. Loathsomeness waits and dreams in the deep, and decay spreads over the tottering cities of men.” The song announces this rise and the arrival of an era when the supernatural and the horrific will come back to rule over mankind, which in Lovecraft's view, is decaying and ignorant, thinking itself an advanced species when human mind can not encompass what is "beyond earth" - and either loses all sanity and/or get subjugated at the sight of such cosmic reach of archetypal sovereignty. It is the beautiful, powerful, passionate song of an entranced, insane and loving cultist.