I'm actually not sure if it was a book series, but there was a question to identify this story several months ago that linked to a website that explained the history and events that took place in this universe.
The setting was in the future in our solar system. There was a plague on Earth, "The Black Plague" I believe, that was killing plants on farms, and it found it's way into orbital farms. There was an event where contact with either Venus or Mercury was lost and the machines on the planet took over. They started shooting at whatever ship came close, then started sending machines out into the solar system to assimilate other machinery.
I also remember a section describing artificial intelligences that are god-like. One in particular, named Gaia I believe, saved the solar system from the machines and plague. There were multiple tiers of existence, or something, with combinations of biological and artificial entities.
I remember a section describing how people who were living around Jupiter didn't really care about what was happening to the inner planets, but the machines that were attacking eventually reached them and it was bad.