At night, having crossed through the window in the North, the witches look up at the Cittàgazze sky where they see angels (last seen going to make war). Ruta decides to follow them and return to destroy the Magisterium. Lyra Silvertongue looks after William Parry who is suffering from the injury by the subtle knife. Lyra goes outside to fill up a water jug but sees Angelica and Paola (who want revenge after the Spectres consumed their brother Tullio) and so runs away, waking up Will, and climbing onto the roof of the café. As the children approach, Serafina Pekkala flies at them, scaring away the children.
In a forest, Will shows Serafina the wound on his hand and also the subtle knife however Will doesn't quite trust her. Serafina says that they will need to use a spell in order to heal the wound. Lee Scoresby and Jopari, in the North of Lyra's world, cross the window in the sky to the world of Cittàgazze. Also in Cittàgazze, Mary Malone talks to the I Ching which gives her some advice. Meanwhile, Lyra talks to Serafina as she gathers plants about witches. Serafina tells her that Will's wound is deep and that they need to travel to Lyra's world for more powerful flora to heal it.
While Mary sits on a boat on the shore, Angelica and Paola watch her and see that the Spectres aren't harming her. Lyra tells Will that she travelled into the new world to investigate Dust after Roger Parslow's death. Lyra sees that Will's hand is bleeding. Will tells her to ask her alethiometer which world his father is in. She finds out that he is in the world that they are in.
Jopari tells Lee about the world they are now in and where they will look for the subtle knife. After getting angry and saying that Lyra is using him as a means to stop, Will apologises and they pause their walk. In Will's world, Lord Boreal and Marisa Coulter cross the window into Cittàgazze. In that word, Mary is exploring and calls out Angelica and Paola (who are spying on her). She gives them a bar which she promises is full of sugar and the girls tell her about the Spectres. Angelica tells her that there are no adults to look after her and tells her that they have seen Lyra. Paola then asks Mary for a hug and Angelica asks her to look after them. After initially refusing, Mary calls after them and says that she'll take them to their adults.
On Lee's balloon, John tells Lee about his world. Lyra tells Serafina that she must help Will find his father. Later, the witches perform a spell which they hope will heal Will's wound. Lyra says that they must keep going up the mountain to find Will's father. At the Magisterium, Pavel Rasek talks to Hugh MacPhail about what he found out with the alethiometer. Fra Pavel tells him that Mrs Coulter is looking for Lyra, who has gone into another world, and that Mrs Coulter asked him to consult the alethiometer as to who Lyra Belacqua is. Pavel tells him that her name (and her destiny) is the same as the mother of humans.
In Cittàgazze, Boreal is nervous due to the Spectres. He and Marisa spy a man who has been consumed by the Spectres and that they could learn from it. In a meeting with Magisterium officials, Father MacPhail says that the Authority has spoken to him and that there is a huge threat looming and that Magisterium has sent troops through the window. He says that Lyra Belacqua will be the first to make a sacrifice in the name of the Authority. In the morning, Will finds his wound has healed. Kaisa tells him that there is a prophecy about Lyra which includes a boy who must travel with her. Serafina reminds him that she's his responsibility too (as he is hers) and must be protected.
Seeing Spectres, Marisa approaches the Torre degli Angeli and reaches out for the Spectres which surround her. Flying over the city, John realises that the knife isn't in the city (as the tower is surrounded by them). However, three Magisterium zeppelins are following them. John tells Lee that the wind is on their side. On the mountainside, Will and Lyra discuss Angelica and Paola and how they might not be as bad as they initially thought. Will tells Lyra that he'd seen children behave like that before when his mother was acting weirdly. He says that he couldn't trust anyone until he met Lyra.
In the café, Marisa offers Boreal a drink and Marisa tells him that, to control them, she hid what made her human. Boreal tells her that they are equal and Marisa kisses him and tells him to drink to that. Boreal, drinking the drink, talks to her about the history of the knife before starting to break up. Marisa tells him that it would have been easier if he had told her that he'd seen Lyra from the start and says that he will only hold her back and that they are not equals. Boreal then dies from the poison in his drink.
Jopari, because he's a shaman, summons a storm as the zeppelins aproach them. As the witches walk along, a Spectre attacks Lena Feldt but Will fends it off with the knife as the witch collapses. After Boreal dies, Marisa holds her hand over a candle as penitance. Following the storm, a fork of lightning strikes one of the zeppelins and Jopari summons birds from the forest to rise up and attack a second. The final zeppelin fires at the balloon and hits the gas canister causing them to fall into the forest beneath.
"Malice" refers to the golden monkey and is not - like many other episode titles - a reference to a chapter in The Subtle Knife. In La Belle Sauvage, Malcolm Polstead said "if that monkey had a name it might be 'Malice'" and the title is a reference to this.
- Main article: His Dark Materials (TV series)#Cast
- Dafne Keen as Lyra Silvertongue
- Ruth Wilson as Mrs Coulter
- Lin-Manuel Miranda as Lee Scoresby
- Ariyon Bakare as Boreal
- Amir Wilson as Will Parry
- Andrew Scott as John Parry
- Ruta Gedmintas as Serafina Pekkala
- Jade Anouka as Ruta Skadi
- Simone Kirby as Mary Malone
- Will Keen as Cardinal MacPhail
- Frank Bourke as Fra Pavel
- Remmie Milner as Lena Feldt
- Sasha Frost as Reina Miti
- Bella Ramsey as Angelica
- Ella Schrey-Yeats as Paola
- Cristela Alonzo as the voice of Hester
- Kit Connor as the voice of Pantalaimon
- Lindsay Duncan as the voice of Octavia
- David Suchet as the voice of Kaisa