Lyra sets out to find out what meaning the cosmic "dust" has for humans. She travels first her world, then ours and finally several parallel worlds.
The Golden Compass (first book)
The main character of the trilogy, Lyra Belaqua, grows up in Jordan College in Oxford. The Oxford in which Lyra lives is not the same as the Oxford of today. Lyra is always in the company of her dæmon, Pantalaimon. In Lyra's world, everyone has a dæmon; it is usually of the opposite gender and accompanies humans in animal form. Lyra's dæmon does not yet have a fixed form, as she is still a child. It is not until puberty that the dæmon assumes a fixed form, and thus also makes a statement about the character of man. Man and dæmon cannot be separated; they are like body and soul. So Lyra lives with male scholars in Jordan College because her parents died in an accident. Her only relative is Lord Asriel, her uncle, but she does not have a good relationship with him.
The book begins with Lyra overhearing a conversation between her uncle and some scholars at the college and learning that the world is on the brink of war. This is prompted by the discussion of "dust," a not-yet-fully-researched matter that imbalances the world and that Lord Asriel, as well as the Church, want to explore further. Dust sticks to people, but not to children, Lyra learns. She is unsettled, but her uncle leaves without further conversation for now. Instead, the college gets a visit from Marisa Coulter, a glamorous, attractive woman who is also extremely successful professionally in a world dominated by men. Lyra is fascinated by her and is delighted when she offers to come to London with her. She allows Lyra a glimpse into the finer things in life, re-dressing her and grooming her hair - all things Lyra didn't get from the men at college. At the same time, the two prepare for an expedition trip to the north, where Lyra is to assist Mrs. Coulter. However, there are also frequent arguments between the two, with Mrs. Coulter's dæmon always acting very aggressively and brutally towards Pantalaimon. After some time with Mrs. Coulter, she throws a cocktail party where Lyra overhears some of the guests. They don't speak very highly of Mrs. Coulter. When Lyra was still at Oxford, children from poor families were always being kidnapped, including Lyra's boyfriend, the kitchen boy Roger. There was a rumor that the Gobblers were hiding behind the actions, but no one knew exactly who they were. Lyra now learns from the guests at the party that Mrs. Coulter founded and runs the General Oblation Authority, so she caught all those kids. Lyra and Pantalaimon no longer trust her and run away.
They join the Gypsies, a people who live on houseboats on the rivers of England. Some of their children have also been captured and they are currently on their way north to retrieve their children. On the journey, Lyra learns that her parents are not dead at all, but Lord Asriel and Mrs. Coulter are former lovers and Lyra is their child. Lyra does not like this at all.
On the way to the Arctic, Lyra meets the armoured bear Iorek Byrnison. He has been stripped of his armor, which is kind of like taking away a human's dæmon. He killed another bear in a fight and lost his position as leader of the armoured bears. Lyra helps him get his tank back, and the two become close friends. Iorek repeatedly helps Lyra in all three parts when she is in trouble, as does Serafina Pekkala, the queen of the Witch Clans of the North. She becomes important again, especially at the end of the trilogy.
Shortly before reaching the fortress of Bolvangar, where the children are being held and experimented on, the Gypters, now on sledges, are ambushed and Lyra is taken by the men directly to Bolvangar. There she meets Roger and also some other children, and learns what is to be done to them there: "Intercision" is used to separate humans and dæmon with a guillotine. This prevents dust from settling on them, which is the main goal of the General Oblation Board and the Church in general, because dust is associated with original sin.
Lyra also faces this procedure; she already sees herself separated from her dæmon when her mother rescues her at the last moment. But Lyra wants nothing to do with her, and makes an attempt to escape with the other children. They are picked up by the Gypsies and Iorek, and the other children travel back home. Lyra and Roger want to visit Lord Asriel in his fortress first, as Lyra thinks he wants the alethiometer. He's not interested in that, though, but all the more interested in her friend Roger, because he needs a child to generate enough energy to build a bridge to a parallel world. Roger dies during the operation, and Lyra and Pantalaimon decide to follow Asriel to the new world.
The titular "Golden Compass" is an alethiometer, an instrument that always tells the truth to those who can read it (including Lyra).
The Magic Knife (second book)
At the beginning of this book we meet Will. He lives alone with his mother, comes from "our" world and accidentally finds a window there, through which he enters the parallel world of Cittàgazze. There he meets Lyra. The town is deserted, and the two soon learn why. The town is populated by ghosts, creatures invisible to children but who attack adult dæmons. Lyra and Will decide to go to Will's world to find out more about dust. There they meet Mary Malone and Lord Boreal. Mary is a scientist and uses her own resources to research dust in her world, which she calls darkmatter. She will play a central role in the third volume. Lord Boreal knows Lyra from Mrs. Coulter's cocktail party. He offers to give her a ride in his car for a bit, and afterwards Lyra realizes he stole the alethiometer from her. They go to him and demand it back. He demands in return that they get him the Magic Knife from Cittàgazze. They agree to the deal and win the knife in a fight; Will loses two fingers in the process. This is the sign that he will be the rightful bearer of the knife. The children learn that the knife can cut through any matter and also open windows into other worlds. With this knowledge, they manage to steal the alethiometer from Lord Boreal's house without having to give him the knife.
Will wants to find his lost father, and Lyra and Will wander off, Will's hand injury forcing them to take repeated breaks. They are accompanied and protected here by the witches around Serafina Pekkala. At the end of the book, Will even finds his father, but only has a few minutes with him, as a witch who used to be in love with Will's father shoots him with an arrow as revenge for rejecting her love out of loyalty to Will's mother. When Will returns to camp, Lyra is gone, but her backpack with the alethiometer is still there.
The Amber Telescope (third book)
The reader learns that Lyra has been taken by Mrs. Coulter to a cave in the Himalayas to hide her from the Church. Her newfound motherly feelings for Lyra have caused her to turn her back on her former employer and now fight against the Magisterium and the Church respectively. She keeps Lyra in a constant fainting state with a potion, as she would never voluntarily stay with her hated mother.
Simultaneously, both Will, who finds Iorek on the way, Asriel's troops and troops of the Church make their way to the cave to kidnap Lyra. By now, it is known that Lyra is the new Eve and there could be another Fall of Man, depending on what she decides. The Church wants to kill Lyra to prevent this from happening. All three parties arrive at the cave at the same time, but ultimately Will manages to save Lyra. They are joined by two of Asriel's spies, the Gallivespier Chevalier Tialys and Lady Salmakia. They keep in contact with Lord Asriel and try to persuade the children to travel to Asriel. But the two insist on going to the World of the Dead first, as Lyra wants to beg Roger's forgiveness and Will wants to meet his father once more. They set out and eventually reach a place where they can enter the World of the Dead - on the condition that the dæmons are not allowed to go with them. The dæmons are separated from their bodies when they die. Under agony Lyra succeeds and also Will, who has no dæmon, but notices how a part of him splits off.
Lyra and Will wander the desolate gray world of the dead, where empty bodies wander hopelessly for eternity. They manage to find Roger and Will's father. As the reader keeps learning how the situation in the other worlds is dramatically coming to a final battle, Lyra and Will decide to free the humans and open a gateway to another world for them. It's a long road, and the children and the Gallivespians are running out of strength, but ultimately they make it. Will cuts a window into another world, allowing the bodies to dissolve into dust and thus reconnect with their dæmons.
Lyra and Will now want to quickly return to their dæmons and the others. Pantalaimon is staying near Lord Asriel and his troops. Asriel has managed to gather a great many warriors from all sorts of worlds, and he now wants to found the Republic of Heaven. He makes his way to Cloud Mountain, where the angels and their leader Metatron live. The latter is God's regent, as the latter is already an incredibly old man who can no longer exercise his rule alone. Asriel, along with his renewed lover Marisa Coulter, manage to outwit Metatron, and they sweep him away into an abyss where they all die. The parents have sacrificed themselves to protect their child and wipe out the Church for good.
Lyra and Will are able to reunite with their dæmons, for by now Will's soul has also turned into a visible dæmon. They return to the world where they opened a window for the dead, for that is where Mary Malone has been living with the Mulefa for some time. They spend some happy hours there, and Mary tells them that she used to be a nun, but then fell in love with a man, and as a result turned her back on the church and became a scientist. Will and Lyra want to look for their dæmons, which they took from the world where the battle against Metatron took place, but then immediately ran away from them. They find them again, but the animals are still a bit shy. Will and Lyra realize that not being in their immediate vicinity doesn't feel bad at all anymore. They take some food with them and decide to have a picnic. In the process, they fall in love with each other after Mary tells them about her own love story.
What follows is a decision that will change the entire world: Together with Mary and Serafina, the children learn that the dust that settles on all intelligent life is about to disappear because, over time, a great many windows have been cut into the worlds with the Magic Knife, and more and more dust is lost through these windows. In addition to this, with every window that is opened, a ghost is created, that is, the beings that depopulated the city of Cittàgazze because they killed the dæmons of the people. They don't attack children because they don't have dust on them yet, so they haven't completed their development. Also, it becomes clear that Will could not live permanently in Lyra's world, and vice versa; the humans must live in their own world or they will die much faster than normal. So the two lovers must decide whether to maintain their own love, leaving at least one window open and thus committing the sin, or to put their own love behind the good of all worlds. After the children close all the windows, there is a dramatic farewell scene: Will closes the very last window and destroys the knife, leaving no way to return to Lyra. Mary promises to look after Will, and Lyra is enabled by Serafina and the headmaster of her former home to go to school in Oxford.
