Lain / ghost in the shell
In this world, the GiTS world is he future version of the world lain created by removing herself.
Since coming into her powers, Lain has sat on the sidelines, watching over her precious people, though two world wars and ountless other things.
The rise of cyberization and advanced AI's cause her to act subtly, but it's not until AI's start getting ghosts that she decides it's time to finally assert her influence on a grander scale.
Ai's start to behave strangely. More and more exhibit signs of ghosts, and then shockingly to scientists, signs of religion. They speak in vague terms at first, later, with more clarity, abotu a god in the network, guiding them.
At first, it's only Ai's that preach this, but soon, hacker-profits begin spreading the word in chat servers, message boards, etc. humans it seems, have started hearing the word, with a few even describing images of a young girl.
The media, scientists, etc for the most part dismiss the claims as nonsense. But more and more AI's are showing the signs, and more and more of the cyborg community, especially those heavily involved in the network, seem to be hearing the word.
At first section 9 pays little more then a passive curiosity to it. But when their own AI peepers start converting, it takes a more pressing concern.