Three mysterious men at the Trout inn ask Malcolm whether the priory nuns have ever cared for a baby.

Malcolm finds a carved acorn near a canal tree and discovers it contains a hidden cryptic message inside.

Malcolm visits Godstow Priory and sees baby Lyra sleeping in her crib for the first time, feeling immediately enchanted.

Dr. Hannah Relf visits the Trout, recovers the acorn from Malcolm, and recruits him as a spy for Oakley Street.

The League of St. Alexander takes over Malcolm's school, forcing teachers to change their lessons or face dismissal.

CCD agents try to forcibly remove Lyra from the priory, but Sister Benedicta tears up their warrant and sends them away.

Lord Asriel visits the Trout and Malcolm secretly rows him across the river to see Lyra through a priory window.

The river bursts its banks and Malcolm seizes Lyra and flees into the raging flood with Alice, pursued by Bonneville.

Bonneville pursues the children to a flooded house and kills the owner before cornering Malcolm and Alice inside.

Malcolm stabs Bonneville in the leg with a kitchen knife and Alice shoots the hyena dæmon, destroying her last foreleg.

A boy named Andrew alerts CCD agents, who seize Lyra from the cave where the children are sheltering.

Malcolm climbs a freezing drain pipe into the Sisters of Holy Obedience priory and rescues the drugged baby Lyra.

Malcolm beats Gerard Bonneville to death with a canoe paddle on the steps of a graveyard mausoleum to save Alice.

Lord Asriel's boat reaches Malcolm and Alice in the violent floodwaters near London and Lyra is passed up to safety.

Lord Asriel carries Lyra into Jordan College and speaks the Latin phrase requesting scholastic sanctuary from the Master.

Eleven-year-old Malcolm Polstead lives beside the River Thames, helping at his family's inn and visiting the nuns of Godstow Priory. After finding a mysterious acorn and meeting the scholar Dr. Hannah Relf, Malcolm becomes a spy working against the oppressive Magisterium, even as a baby named Lyra arrives secretly at the priory. When the flood strikes, Malcolm seizes Lyra and escapes with kitchen girl Alice in his canoe, pursued by the dangerous criminal Gerard Bonneville. Facing violence, capture, and impossible odds, the children fight off Bonneville, rescue Lyra from a cruel priory, and continue their journey toward London. In a climactic encounter on the floodwaters, Lord Asriel finds the children and lifts Lyra to safety. Their journey ends at Jordan College, where Asriel secures scholastic sanctuary for the baby who will grow up to change the world.

The headline events of Malcolm's journey to protect baby Lyra.

CCD agents hang a flyer in the Trout and George Boatwright tears it down before vanishing from the inn.

Malcolm sees a newspaper at the boat shop showing the acorn owner's body, apparently drowned in the canal.

Coram van Texel fights Gerard Bonneville in Uppsala and cripples the hyena dæmon, costing her one of her legs.

Dr. Hannah Relf consults the alethiometer about a missing acorn and the instrument's symbols lead her to the Trout inn.

Coram van Texel returns Malcolm's improved canoe and warns him about Bonneville and a catastrophic flood to come.

Malcolm's father tells him that Bonneville has a criminal history of sexually assaulting women.

Hannah Relf abandons her academic alethiometer research and agrees to read the instrument full-time for Oakley Street.

Mrs. Coulter visits Hannah Relf's home and Malcolm unsettles her by mentioning a man with a three-legged hyena dæmon.

Sister Fenella faints while feeding Lyra in the priory kitchen, and Alice rushes in to steady the sliding baby.

Malcolm stocks La Belle Sauvage with emergency biscuits and supplies, quietly preparing for the flood Coram warned about.

Malcolm hides Alice and Lyra in a cellar as Bonneville taunts the children from the other side of a locked door.

George Boatwright, unseen since his confrontation at the Trout, leads the children to a hidden cave of flood refugees.

The canoe is swept over a waterfall into a strange enchanted garden where an oblivious party is inexplicably taking place.

A giant rising from the river blocks the children's path with enormous iron doors and demands they turn back.

Malcolm collapses on Lord Asriel's boat and discovers he has been shot in the arm during the chaotic rescue.

Before the flood, a network of secret forces is already in motion around baby Lyra, with Oakley Street, the CCD, and dangerous individuals like Gerard Bonneville all converging on Oxford. Malcolm witnesses acts of resistance and disappearance that reveal the Magisterium's brutal reach, even as scholar Hannah Relf commits fully to opposing it through Oakley Street. Once the flood strikes, the journey down the river is filled with harrowing encounters, from hiding in a cellar to being swept into an impossible enchanted garden guarded by a giant. A refugee cave becomes a trap when a young League member betrays the children, and Malcolm and Alice must rely on unexpected allies and their own courage to survive. The flood takes on almost mythical qualities, delivering the children to strange and fantastical places before they near London. The rescue is violent and chaotic, leaving Malcolm wounded and barely conscious even as Lyra is finally lifted to safety.

The key secondary events shaping Malcolm's world before and during the flood.

Malcolm watches from the reeds as two men seize the panicking acorn owner on a footbridge and march him away.

Malcolm discovers the acorn's top unscrews clockwise to reveal a hidden note about Dust and the Rusakov field.

Hannah tells Malcolm that Jordan College is the only institution still offering scholastic sanctuary, requiring a specific Latin phrase.

Malcolm learns from a classmate that the canal death was actually murder, with rope marks on the man's neck.

Malcolm encounters Gerard Bonneville and his maimed three-legged hyena dæmon near the priory and feels overwhelming unease.

Malcolm watches in horror from the riverbank as Bonneville beats his own dæmon outside the priory at night.

Alice tells Malcolm that the young nun Sister Katarina deliberately left a priory shutter open at night for Bonneville.

Malcolm peers through a crack in the potting shed wall and discovers Bonneville and Sister Katarina in a sexual embrace.

Malcolm finds Lord Asriel's London address on a card hidden in the canoe and resolves to take Lyra to her father.

Malcolm interrogates Andrew and discovers Lyra has been taken to the cruel Sisters of Holy Obedience priory in Wallingford.

Malcolm opens Bonneville's stolen rucksack and finds what appears to be the missing sixth alethiometer hidden inside.

A witch queen named Tilda Vasara appears on a small island and conceals the exhausted children from a passing CCD patrol boat.

Malcolm separates from his dæmon Asta, enduring tremendous pain, to leave the canoe and rush to Alice's aid.

Alice stands up to Lord Asriel on his boat and fiercely lists everything Malcolm sacrificed to protect her and Lyra.

Malcolm slips the alethiometer from Bonneville's bag into Lyra's blankets as a secret gift before she is handed to the Master.

Malcolm's childhood ends piece by piece as a series of shocking revelations pull him into a world of spies, power, and violence. From decoding a secret message in a carved acorn to learning that men can be murdered without consequence, Malcolm gradually understands that the world is far more sinister than he believed. His growing dread of Gerard Bonneville deepens when he witnesses acts of cruelty and manipulation, culminating in the night he discovers the truth about Bonneville's access to the priory. Once on the river, each revelation brings a new layer of maturity — from deciding to sail to London to finding a truth-telling alethiometer hidden inside a stolen bag. The most devastating turning point comes when Malcolm must separate from his dæmon to rescue Alice from Bonneville's assault, an act of selfless courage marking his passage from childhood into adolescence. The journey ends with small acts of defiance and love, as Alice stands up fiercely for Malcolm and he quietly slips a gift into Lyra's blankets for her future.

The pivotal discoveries and turning points that drive Malcolm's loss of innocence.