Into this wilde Abyss,
The Womb of nature and perhaps her Grave,
Of neither Sea, nor Shore, nor Air, nor Fire,
But all these in thir pregnant causes mixt
Confus'dly, and which thus must ever fight,
Unless th' Almighty Maker them ordain
His dark materials to create more Worlds,
Into this wilde Abyss the warie fiend
Stood on the brink of Hell and look'd a while,
Pondering his Voyage; for no narrow frith
He had to cross.
~Paradise Lost, Book II, John Milton
Thus begins Satan's descent to Earth and his mission to cause the Fall of Man. Phillip Pullman uses the epic battle of Heaven and Hell as an underlying theme in his fantasy-steampunk-coming of age trilogy, His Dark Materials. The Golden Compass introduces the reader to Lyra, Pantalamion (her daemon), and her alternate-history world of Oxford, London, and Lapland; there are some spectacularly bad people in Lyra's world (Lord Boreal, Mrs. Coulter, and Lord Asriel, just to name a few) as well as some spectacularly good people and giant, talking, armoured polar bears to boot (Iorek Byrnison, FTW!!). There is also Dust, a strange particulate that is attracted to adults but not children. The Subtle Knife introduces a new protagonist, Will Parry, who lives in our Oxford. He meets up with Lyra in a strange world, Citt'gazze, and becomes the posessor of the Knife; the Knife has such a fine edge that it can cut through the fabric of space to make a window into another world. The children also meet Mary Malone, a former nun who researches mysterious particles (the Dust of Lyra's world). The Amber Spyglass (awarded the Whitbread Award in 2001, Pullman is only children's author to have received the prize) finds the major characters of the series readying for a battle between the Kingdom of Heaven and Lord Asriel. At the heart of the conflict is Lyra, who must "fall" or grow-up to save all the worlds and prevent Dust from disappearing forever.
There are many thematic elements in His Dark Materials. Pullman's Church is obsessed with the prevention of "sin" aka knowledge; this is why Dust is attracted to adults and not children. Dust is self-awareness and knowledge through experience (also, the difference between innocence and experience, expressed in the poetry of William Blake). The Church is trying to rid the world of "experience" - hence the insane project to separate children from their daemons. The Church of Pullman's novels also abhors physical pleasure, whether through the enjoyment of foods or physical comforts or sexual awakening. Lyra is a second Eve, one who must "fall" to save knowledge and self-awareness from becoming lost forever. She is destined to do this even though she herself is not aware of this destiny until almost the end of the trilogy. Although Lyra and Will are the Eve and Adam of the story, they must ultimately part because neither can live in the other's world for extended periods of time.
Pullman comes down hard on absolutist religious dogma; although His Dark Materials uses a largely Judeo-Christian background, the message about absolutism applies to any fundamentalist religion. It doesn't set well with some people - the Catholic League went after the trilogy for promoting atheism when the 2008 film adaptation of The Golden Compass was in theatres (books aside, that was a terrible adaptation, just awful plot adjustments). If someone wants to have His Dark Materials removed from public school classrooms and libraries, I think Paradise Lost should go as well as The Chronicles of Narnia. Turnabout is fair play; not everyone drinks of the communal wine and the parent, not the school district, should be the one who decides whether their child should read a more philosophical work. I said public school because a private school of religious affiliation is allowed, under freedom of religion, to have a tighter grip over materials at the school (and one wouldn't enroll his/her children at a religious school unless one agreed with the curriculum/religious viewpoint and, besides, public libraries can suffice if a parent wants his/her child to read a book the private school finds questionable in that instance).
I'm all for children reading His Dark Materials. Pullman's writing is very sophisticated and he doesn't dumb down any of the philosophical elements just because the series is meant for children. The Golden Compass is more straightforward than The Subtle Knife which is more straightforward than The Amber Spyglass; by the time younger readers reach the third book they will be ready for the themes introduced. I found myself reading very carefully by the time I reached the third book of the series because I didn't want to miss anything (there's a lot going on in The Amber Spyglass).