In the second book we meet Will, who is from our world, and he and Lyra run into each other in another world. Will found a door in his world. The world that they are in is infested with Spectors, who feed on peoples souls. Only children are not affected by them because children have not sinned yet. Will become the bearer of the Subtle Knife, which is a knife that can cut doors that open new worlds. Little do Lyra and Will know is that every time Will makes a cut, the knife is creating another Spector.
Apparently we find out that Lyra is really Eve. The Magesterium wants to find her and kill her before she commits the original sin. If Lyra commits that sin, then dust will live on forever. Dust is what the Magesterium believed to be the cause of sin. Dust is your soul. In Lyra's world their souls are on the outside in the form of daemons. Every single world has dust, which means that everyone sins. In the first book the Magesterium tried intercision, which is cutting daemons away from children so that they don't sin, but it turned out ugly because people can not survive without their souls. Most of the last book, The Amber Spyglass, was about how all the worlds will eventually disappear because the dust in leaving the worlds. It is being sucked into this huge abyss that the Authority created.
Since the Authority has been in charge, everyone who dies is kept in this dark nasty world where the dead are constantly being tormented by harpies. Lyra and Will travel to the world of the dead and eventually recuse the dead by cutting a door they can escape through. In order to do this, Will and Lyra has to leave behind their souls. Lyra had to leave her daemon, Pan.
The Magesterium fails in killing Lyra so she does sin. Her and Will fall in love. They grow up and are now prey to the Spectors. They find out why there are Spectors so an angel comes and helps them close all of the doors that knife has created. Lyra's parents, Mrs. Coulter and Lord Asrial both die in a battle against Megatron (which is a really odd name), who is the head Angel on the side of the Authority. In order to protect everyone and save dust, Will and Lyra will not be able to see each other anymore. A person can only live their entire life in their own world. Lyra and Will have to separate because they need to leave the door open they created for the dead.
Everyone has to make sacrifices for life to go on. Things are done because they are the better choice. People need their souls to survive and our souls are responsible for our sins. But without sins, we would not have souls and it would just be worlds full of zombie like people who are slaves to God. To sum it up, organized religion is bad because it is trying to control everyones lives. In order to be free from it we must rebel and have a war and hope that you win. I agree to an extent, but I am not one to bash God so I wont. And, once again, children are responsible for saving the world. Love it when that happens. Be yourself and do not let anyone control who you are and who you become.