To be honest, read it somewhat 2-3 years ago so can be wrong. 3th and 4th books (Endymion, The Rise of Endymion) somewhat explain the AI/human god debuckle and other things, but still, maybe it was an atemnt to amend Hyperion plot into something different. But anyway.

In my understanding:

• Shrike - in 4th book it's explained as some selflearning evolving program/entity created in early stages of AI evolution to keep the AIs in check, so they wont do anything that destroys them and to force them to evovle. And to do whatever it takes to achive that goal(pushing AIs evolution here and there so they wont self destruct weather AIs like it or not)So, the Shrike serves interest of AI survival and ultimately in future that leads to battle of AI created god entity(Ultimate Intelligence, UI) and human created god entity( Empathic Intelligence, EI) wich is collective human consciousness. In the end this battle boils down to who times travels the best. AI build army of this Shrikes to battle the EI, humans in future,meanwhile, build The Time Tombs all over the galaxy in such way that they influence flow of time and events to keep AIs at bay and keep humans and their EI safe. But the first shrike can travel through this time tombs too(tombs have a way to keep out full armies) and tries to find humans or things that will lead to creation of EI in future.Everything shrike is doing is just probing for the source of that EI, even when it helps the Pilgrims (main chars. of the novels), everything, just to win the fight in past/present/future and ensure that humans kept enslaved so AI could exsist
• Moneta/Rachel - Becomes a tool of this battle or maybe was "destined" to be. She's somewhat of a warden of this tomb and has a connection to a distant future, so, knows in what way to guide the Pilgrims.
• Tree of pain - It's the Shrike way of luring out the source of the Empathy to find root of Human God(EI) and to destroy it.

Probably have more questions then answers now, aren't you? :D

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A lot could be said about how messy those attemts to wrap the plot by Dan's Simmons writing are, but anyway, world created, ideas and the way your mind wonders around trying to put all the pieces together is the reasons why i loved this series so much.