The Church of the New Sun was originally created by Rick Reynolds (under the name of "Reverend Gary") on the order of the Gods in order to acquire a large number of Enlightened in order to perform a sacrificial ritual which would allow the Gods to trap and imprison Aten as part of a secret "Project Orion". However, Aten and Fenrir's agents became aware of those efforts, took over the project, and mind controlled Rick Reynolds. The Church then work to use that same Ritual, but in order to destroy Selene instead.
A group of Godborn put an end to the Church of the New Sun's efforts and freed Rick Reynolds. It was then taken over by Hapi, and made to serve the Gods and heal the ills of humanity.