Minor spoilers for Stross' Laundry Series follow.
In The Jennifer Morgue, we are introduced to the Deep Ones. In The Apocalypse Codex they are mentioned multiple times to be somehow connected to one of the Cults that wants to awaken the Sleeper in the Pyramid.
However, in The Jennifer Morgue the Deep Ones are presented as being basically sane and having as much to lose from CASE NIGHTMARE GREEN as humanity. So what's the deal? Did I miss something, are they different groups, is it referenced anywhere clearly?