Xaphania narrates about the Authority, who has ruled for many millennia in the kingdom of Heaven.

The one who called himself the Almighty, the Creator, is just an angel who rules with a dark angel by his side. The angels who fought for truth were cast out of Heaven and have lived between the worlds ever since, waiting for vengeance.

An ambitious mortal man (Asriel) is assembling an army to go to war on Heaven. A new Eve has emerged, and rebellion is coming.

Will searches for Lyra across many worlds, using the subtle knife to travel and the alethiometer to guide him.

Lyra dreams of being in a dusty, yellow world. Pan is not with her. She hears Roger calling for her, but she cannot see him.

Lyra sleeps in a stone chapel nestled in a rocky cliff. She hears her mother whisper her name.

Asriel and Stelmaria travel between worlds in a flying machine -- the intention craft. The craft cannot withstand the dimension jump, and they crash land.

Near the stone chapel, a young girl -- Ama -- with a squirrel daemon, carries herbs and flowers in a bag. Mrs. Coulter spies the girl and greets her in sign language.

Ama is apprehensive of her, signing that the chapel has been empty and there are rumors of someone hiding there. Mrs. Coulter explains that she is not hiding and asks Ama to follow her in.

Reluctantly, Ama follows Mrs. Coulter into the chapel. Mrs. Coulter takes the girl to Lyra, who is asleep. Mrs. Coulter explains that her daughter Lyra is under a sleeping spell, and she needs time to help her wake up.

Mrs. Coulter asks Ama if she will help keep people away and keep the secret. Ama agrees to help and hugs Mrs. Coulter. Ama leaves. Pan weakly asks for her to let them go. Mrs. Coulter gives Lyra more "medicine."

Will reads a map when he senses a presence behind him. He sees nothing, then draws his knife and goes to a different world.

Will consults the alethiometer. Two angels -- Balthamos and Baruch -- appear before him, telling him not to be afraid, and they wish to talk. He tells them to stop following him and leaves the world using the knife. Will finds himself in a barren, grey world.

Asriel is scratched up but unharmed. The craft is beyond repair. Along with Stelmaria and several Gallivespians, Asriel heads into a prison, fighting his way through until they defeat all the guards.

Asriel asks the prisoners which one of them is Commander Ogunwe. Ogunwe pulls a key from one of the fallen guards and releases himself from his cell, introducing himself to Asriel.

Asriel introduces himself. Ogunwe refuses to help in Asriel's war on Heaven. Stelmaria entreats him to listen. Asriel says he wants Ogunwe's army as well as his leadership.

Father President MacPhail arrives in Geneva. Three young Fathers -- Jerome, Gomez, and Heyst -- greet him. Father Jerome tells him of the arrest of a poet who had been reading from a book of poetry in public and inciting discussion. Jerome presents MacPhail with the book in question. MacPhail asks what should be done. Jerome says the author will be imprisoned for heresy. Heyst tells him that all material in the building has been confiscated and all attendees imprisoned. At MacPhail's question, Gomez suggests physical atonement in public.

Baruch and Balthamos find Will in the grey world. They explain they can dimension-hop because they are made of dust. They have been searching for Will, the Æsahættr, because a war is coming, and he has the weapon that will help them win.

They tell him Lord Asriel is amassing an army. Will refuses, saying he knows what is "supposed" to happen, but he will not fight alongside Asriel, as he is searching for his lost friend Lyra, Asriel's daughter.

Balthamos says they will keep following him. Will asks them to help him find Lyra, and then he will go with them. Will shows them the alethiometer, and Baruch assures him that they will be able to find Lyra.

Lyra dreams of a large warehouse where zombie-like people shuffle slowly forward. Lyra sees Roger, and they call to each other, but she loses him in the crowd.

Ogunwe leads Asriel to his hidden base. Ogunwe sees his daughter, Machi, and greets her joyfully. Asriel watches. After catching up with Machi, Ogunwe returns to Asriel. Asriel asks how long it has been since he saw his daughter. Ogunwe says he was in his cell for over ten months.

Ogunwe asks Asriel who the war is truly against and what he wants from him. Asriel says the Authority is the enemy. Ogunwe is dubious, saying it is impossible, but Asriel insists, saying the Authority is merely an angel.

Asriel explains that a thousand years ago, there was an angel who discovered the Authority's secret -- her name is Xaphania, and she sits on his council.

Ogunwe says he cannot help. He takes Asriel to meet his older daughter, who was taken for "training" and was brainwashed by the Authority. Ogunwe wants to stay to save as many children from his world as possible.

Asriel examines Ogunwe's older daughter, saying her daemon has been severed. Asriel explains how a daemon is like a soul, and the girl's soul has been removed, so she is a mere shell.

Drones appear overhead. Ogunwe commands everyone to get underground while he and Asriel arm themselves.

MacPhail and Gomez meet privately. MacPhail explains that Fra Pavel's alethiometer has prophesied darkness threatening to overtake the world, which has led MacPhail to Geneva. It is the girl Eve, the cause of all sin, and if the serpent tempts the girl, sin and dust will triumph.

Gomez asks where the girl is so that they can stop her. MacPhail says Pavel has not yet discovered her location, but when he does, MacPhail would like Gomez to lead the troops. Gomez accepts the honor. Gomez offers to drop in on Fra Pavel to "speed him up."

Mrs. Coulter mops Lyra's brow. Pan begs for her to release them. She refuses. Mrs. Coulter goes outside and stares at the water.

In the grey world, Baruch attempts to decipher the alethiometer. Baruch discerns that Lyra is in the world of the daemons, being held captive by a woman in a house carved into rocks on an island in the German ocean. Will asks about the woman's daemon.

When Baruch tells him it is a golden monkey, Will realizes Lyra is with her mother and, therefore, in danger. Balthamos will go with Will to seek Lyra, while Baruch will go to Asriel, though Balthamos is concerned about the danger. The angels kiss.

Baruch asks that as soon as Will and Lyra are together, they should come to meet him and Asriel. Baruch leaves. Will and Balthamos pass into a new world together.

Father Gomez meets with Fra Pavel, asking for the girl's location. Pavel admits to having difficulty with the final part of the reading. Gomez suggests reeducation for Pavel if he cannot figure it out. Pavel promises to find her.

Pan wakes Lyra. Mrs. Coulter is asleep. Lyra struggles to get out of bed. The golden monkey watches. Lyra stumbles through the chapel and manages to get outside. She hears Mrs. Coulter calling. Lyra crawls to a hiding spot.

Mrs. Coulter and the golden monkey emerge, calling for Lyra. Mrs. Coulter sits beside Lyra and sympathizes with her state but insists she is doing this to keep Lyra safe from the people coming for her.

Mrs. Coulter chloroforms Lyra. Ama watches from a hiding spot.

At Ogunwe's camp, Asriel tries to convince the Commander that the Authority needs to be taken down. Ogunwe doesn't even believe in other worlds.

Asriel says that the Temple and the Magisterium are just arms of the one Authority at the center of it all. Ogunwe remains skeptical. Asriel offers to show him by taking him to another world.

Lyra sleeps while Mrs. Coulter stares out at the sea.

Balthamos asks Will how Lyra could read the alethiometer when it takes men many years of study to be able to interpret it. Will explains that the alethiometer is to Lyra what the knife is to him.

Will and Balthamos arrive at a port in search of a ship. They see an armored polar bear, Iorek Byrnison, fighting the men, yelling, "Where is she?" Will recognizes the bear as a friend of Lyra's.

Will stands in front of the bear, asking him to stop. Iorek says they have taken one of his bears. Will asks to fight Iorek in single combat, saying if he wins, Iorek must leave them all alone -- if Iorek wins, he can do what he likes to any of them.

Iorek says it would be shameful to fight such a weakling, so Will asks for a piece of his armor. Iorek gives him his helmet, which Will then slices cleanly with the knife. Iorek says he can not fight the knife and forfeits. Will orders the people to free the other bear, and they do.

Will informs Iorek that he is searching for Lyra. Iorek agrees they must go to her.

Gomez visits MacPhail and tells him he saw Fra Pavel, who had now divined that the child is with her mother. Gomez is confident he can secure the child, though he will use unsanctioned methods.

MacPhail tells him to do so and bring the girl and her mother directly to him. He reminds Gomez not to trust Mrs. Coulter. Gomez assures him that he will do what it takes and kisses MacPhail's hand.

Gomez prepares to leave, using a mechanical insect to "sniff" Lyra's clothes and track her down.

Mrs. Coulter watches Lyra sleep.

Will, Iorek, and Balthamos head out to sea on a boat.

Asriel creates a gateway to another world, leading Ogunwe to his "Republic of Heaven."