I recently finished reading the next book in Pullman's His Dark Materials series. The Subtle Knife is the sequel to The Golden Compass, and now I clearly see why the church has its panties in a twist about these books.
In this book, we follow Lyra as she hops between worlds. In her travels she (and we) learn that Lord Asriel is planning to mount an army that can succeed where previous attempts have failed - to overthrow the ultimate Authority (i.e. God). He is moving between worlds to assemble the most intimidating army possible in accomplishing his task.
Ahem. These are definitely weighty matters for young adult fiction.
During Lyra's journeys, she meets Will Parry, and young boy with his own role to play in these large events. Will becomes the chosen bearer of the subtle knife, which is the only known tool that can open doorways between worlds. (So now, Lyra is the bearer of the golden compass, and Will is the bearer of the subtle knife.) We know that their destinies are entertwined, but we are not completely sure how.
By the end of book 2, the reader is still not certain which "side" Pullman is espousing - the side of the "Authority," which man seems to have perverted into an increasingly dictator-like theocracy; or the side of Lord Asriel, the contemporary rebel whose actions are shaking the very particles that make up reality.
Intrigued, I did a little research on Pullman and his thoughts. (You'll remember that he got tons of press when the movie came out.) Check out this interview. It's really long, but it has helped me understand Pullman's philosophy a bit better.
I am pressing on. I plan to read the final book in the series - The Amber Spyglass - next.