Children of an Elder God

Children of an Elder God by John Biles and Rod M. is a Neon Genesis Evangelion/H.P. Lovecraft Fusion Fic.

Neon Genesis Evangelion is essentially "Giant Eldritch Abominations vs. Giant Robots battle to the Apocalypse" with some deconstruction and weirdness thrown in, so it only stands to reason that someone would throw Cthulhu and all the rest of the Great Old Ones into the mind-screwy stew.

The first 23 chapters can be found here, and chapter 24 can be found in two parts on Spacebattles.com here and here.