This is the second half of my discussion of the trilogy His Dark Materials.
See my post on The Golden Compass.
I do not want to put off anyone from reading this trilogy. The last two books, The Subtle Knife and The Amber Spyglass, are much less subtle than The Golden Compass, but the trilogy remains highly imaginative, enjoyable regardless of what you think of religion. I mean, I don't even completely agree with them myself. Also, I would like to put to rest a popular misconception about these books. No, they do not kill God. If you didn't know that, I recommend skipping my spoilers and reading the trilogy instead.
Spoiler Alert for the His Dark Materials trilogy
The Church adopts a much more sinister quality as compared to the first book. For example, one character performs "preemptive penance," which absolves him of future sins, allowing him to be an assassin. It also turns out that the Church is simply a pawn of the Authority, who controls churches in all the parallel worlds. The Authority, by the way, is not God, but the oldest angel, who had claimed to be God. The Authority is senile, and actually lets another angel, Metatron, rule for him. Metatron is a tyrant dictator, and the biggest antagonist of the series. I can't help but think that Authority and Metatron are supposed to be symbolic of moderate and extremist religion respectively, for their story echoes the common freethinker sentiment that moderates "enable" extremists.
You often hear that Pullman killed God in this trilogy, but that's completely false. Technically, they only killed Metatron, the Regent of an angel that falsely claims to be God. I totally missed it when I read it, but apparently the Authority also died. He died unspectacularly, simply dissipating in the wind. The missability of the Authority's death is Pullman's way of belittling the fraud.
After defeating Metatron, Pullman sets up what he calls the "Republic of Heaven" as opposed to the "Kingdom of Heaven." Pullman is not destroying heaven, but improving upon it. Pullman seems to think that religion has unfairly monopolized heaven, spirituality, and whatnot. He thinks religion, just like the Authority, is a fraud claiming to be divine. The stories strongly suggest that there is something truly divine, but Church is not it.
In my opinion, the real God in this trilogy is Dust itself. Pullman adds a lot more creatures, each of which is not only interesting in its own right, but is also designed to further describe Dust. Spectres are evil creatures that eat Dust, leaving pure apathy in their wake. Angels are beings made of condensed Dust, but not blessed with material bodies (more rebuttal to C. S. Lewis' "hatred of the physical world"). [Interestingly, Pullman inserted a gay angel couple, which I'm sure upsets many conservative Christians.] The Mulefa are creatures that evolved to roll on wheels (a detailed explanation followed). When the Mulefa found a way to access Dust, they became conscious and gained a permanent collective memory. Yes, Dust pretty much makes up all that is good in the world.
The anti-religious themes don't stop there. In their adventures, Lyra ends up destroying the afterlife, which it turns out was hardly paradise. It's a not-so-subtle attempt to argue that the materialist view of the afterlife is actually better. Later, Lyra reenacts the Adam and Eve story and then... There was more blatant allegory, but I forget the rest.
But like the first book, there's a lot more to the themes than just regular old anti-religion. For example, there is one character from our world who discovers Dust not through theology, but through particle physics. She finds what she calls "Shadow Particles" (aka Dust) that seem to hang out only around humans and human-designed objects. It acts as if it were conscious. However, her discoveries are so unbelievable that she loses funding. If this book is critical of religion, it's critical of science as well. It asks us, could science ever prove God?
So I've been calling all these themes "anti-religious", but is that what they are really? Are they anti-religious, anti-dogma, anti-Christian, anti-God, or what? I would say The Golden Compass is mostly anti-dogma (which is only anti-Christian if you think Christianity is all about dogma), but these books are arguably much stronger. Before, the Church was just misguided, and would justify evil acts with close-minded ideals. Now, the entire belief system of the church turns out to be a sham. It's still anti-dogmatic, but it also suggestively connects dogma and nearly all of organized religion.
Whether that means that Christians are justified in boycotting the movie... well, I'll let the reader decide that one.