Maile Meloy’s 2011 New York Times bestseller The Apothecary is the first in her young adult trilogy, which also includes The Apprentices (2014) and The After-Room (2017). This novel merges the genres of historical fiction and magical realism, and it was named one of Publishers Weekly’s Best Children’s Books of 2011. In 2012, The Apothecary also won the E. B. White Read-Aloud Award and the California Book Awards YA Gold Medal. Set in London after World War II, The Apothecary honors children’s intelligence and loyalty’s power while highlighting the possibilities for magic in a world where mysticism seems divorced from science and reason.

This guide refers to the 2011 Puffin Books paperback edition.

Content Warning: The source material and guide feature depictions of death, ableism, and gender discrimination.

Plot Summary

Jane “Janie” Scott, as an adult, writes a letter to readers explaining that she lost her memory of the events depicted in the text that follows but that her diary allowed her to recall them. The text then flashes back to her childhood.

Janie is seven when World War II ends, and her parents—Marjorie and Davis—are optimistic about the future. However, as postwar fears of communism grow and the US government begins persecuting suspected communists, Janie’s parents tell her that they’re moving from Los Angeles, California, to London to avoid having to testify about their friends. In England, Janie’s parents use fake names and work as writers for the BBC. London is gray and scarred by bombs, and Janie misses California. She and her father visit an apothecary shop, and the man there offers her something to help with her homesickness.

At St. Beden’s grammar school, Janie meets Sarah Pennington, a rich and beautiful girl in her grade. Sarah takes Janie to Mr. Danby’s Latin class, explaining that he was a pilot in the war. At lunch, a boy named Benjamin Burrows refuses to participate in a bomb drill, citing its uselessness, and Janie admires his bravery. After school, she’s supposed to meet her parents but sees Benjamin inside the apothecary shop. She realizes that he’s the apothecary’s son but doesn’t want to become an apothecary himself. Later, she catches Benjamin following her, and they talk. He says that he wants to be a spy. He asks her to meet him at school on Saturday afternoon, and Janie tells her parents about him.

On Saturday, Benjamin takes Janie to the park, telling her to watch the man on the bench behind him. The man, Leonid Shiskin, is a Soviet accountant and the father of Sergei, a student in Janie’s Latin class. Benjamin says that Shiskin passes messages to people in his newspaper. A well-dressed man joins Shiskin, and Benjamin and Janie follow him to a hotel, where a clerk calls him “your excellency.”

The next day, Shiskin is on his bench when Janie and Benjamin arrive. Soon, the apothecary joins Shiskin, takes the paper, and leaves. He reads a note and throws it away. Janie and Benjamin follow him to the shop and find him burning papers. The apothecary (Mr. Burrows) has no time to explain but says that he must hide “the book.” Someone rattles the door, and Burrows gives that book, the Pharmacopoeia, to Benjamin, forcing him and Janie into a cellar. They hear men speaking German and see a man who has a distinctive scar. When the intruders leave, Benjamin and Janie go to the Scotts’ apartment, and they let Benjamin spend the night.

Benjamin realizes where he saw the Pharmacopoeia’s symbol before. On Monday, they go to the Chelsea Physic Garden and find the book’s symbol on the gate. An elderly man (the gardener) recognizes Benjamin. They show him the book, and he tells them about Jin Lo, a Chinese chemist. The gardener points out different recipes that sound like magic. Benjamin doesn’t believe that they work, but the gardener cautions him to keep an open mind. Janie suggests that they use the “Smell of Truth” recipe on Shiskin, and the gardener tells them what to do.

At Shiskin’s house, Benjamin and Janie prepare the potion and ask Shiskin to smell it, but he recalls seeing them at the park. He says that the scarred man works for the East German secret police. Shiskin admits that Burrows is supposed to meet him in two days. Returning to the garden, the children find the gardener critically wounded. Before he dies, he says to avoid the police and points them toward a small bottle hidden in the garden. Janie grabs it as they flee. That night, she writes in her diary, and they inspect the bottle, which contains an avian elixir. Janie learns that her parents must leave town for a few days.

Janie tells Mr. Danby about the Pharmacopoeia. At lunch, a police officer and detective come for Janie and Benjamin, who pass the book to Sergei before being taken to Turnbull Juvenile Court. They meet Pip, a pickpocket and housebreaker. Danby arrives, apparently from the Foreign Office, but they realize that the scarred man is driving Danby’s car. The children run back inside, and Pip leads them to the roof; Janie suggests that they use the avian elixir. They all turn into birds and follow Danby’s car to a secret bunker. When they turn back into children, Janie suggests that they make themselves invisible to get inside. They go to St. Beden’s and get the book from Sergei. When Pip meets Sarah, he instantly falls in love. She clearly likes him too.

At the chemistry lab, they make the invisibility serum. They add it to water in a clean garbage can and, one at a time, undress and climb in. Now invisible, they run to the bunker. They sneak inside and, finding Jin Lo imprisoned, free her; she creates an orange smoke flare, while Pip picks the lock. They flee the bunker and go to the apothecary shop, where they find a small pile of salt in a tiny bomb shelter. Jin Lo explains that the salt is Benjamin’s father and mixes a big pot of potion, adding the salt. She stretches the resulting goo, and Burrows emerges. The group hides in the physic garden until morning. Burrows explains that he and Jin Lo are working on a way to contain a bomb’s blast. To absorb its radiation, he’ll use the “Quintessence” of the jaival tree’s flower, but he must harvest its blooms in the morning. The Soviets are testing a new bomb, and Jin Lo and Count Vilmos, or “Vili,” a Hungarian physicist, have come with the man from the park bench to help Burrows. He forces the tree to bloom, but it emits black smoke, as if in disapproval. Burrows says that this is called the “Dark Force.”

The children go to St. Beden’s to get the Pharmacopoeia, and Sergei tells them that the Soviets will kill his mother and sister unless his father helps them. Benjamin, Janie, and Pip are determined to get on the ship where Sergei’s family is being held. Pip suggests that they ask Sarah for heavy clothes for the trip, and they make more invisibility elixir. They go to Sarah’s house, and her butler delivers a trunk to the ship, where Burrows also is. At the port, they meet Vili. They give Burrows the Pharmacopoeia, and he makes them disembark. The children break into a nearby home to use the bathtub, but only Benjamin and Janie get to use the invisibility potion. Outside, Pip distracts the police, and Janie and Benjamin sneak onto the ship. When Jin Lo finds them, they tell her about Shiskin. She confronts Shiskin, and they tie him up. The children explain everything to Burrows, and he asks the crew to continue the mission. They agree and disguise the ship by painting it red and renaming it after a crew member’s daughter.

The next morning, Janie asks Shiskin to help them, but he grabs her when she unties him. She yells, and Vili and Benjamin rush in. Shiskin points a gun at her head, but the count freezes time, rescuing Janie and taking Shiskin’s gun. After they lock him up again, Jin Lo practices catching particles with her polymer net, and Vili tells Janie about Andrei Sakharov’s bomb. He explains that the Dark Force is the consequence for tampering with natural laws.

Burrows’s group must flee when the crew spots a patrol vessel. They use the avian elixir and fly to the island. Janie squeezes into the building where the bomb is, but the scarred man captures her, and he and Danby take her to their ship. She returns to her human shape, and Danby decides to let the bomb’s radiation kill her. Janie, watching from the boat, sees it detonate, but then its mushroom cloud contracts. Janie, Danby, the scarred man, and Sakharov take a helicopter back to the island and see Benjamin falling from the sky; Janie tells Danby that Benjamin knows all the apothecary’s secrets, prompting his rescue. In the helicopter, Janie sees the Dark Force approaching them. It envelops the helicopter, and Janie and Benjamin fall out. She refuses to leave him, and a Norwegian man rescues them from the water.

The man takes care of them before returning them to their ship, and they take a plane to London under assumed identities. Benjamin recovers, and Burrows drops Janie off at home. The next morning, Benjamin calls, inviting the Scotts to meet him and his father at the train station; he asks Janie to bring her diary. Pip comes too, and Burrows proposes a toast to their success. He says that the country is no longer safe for him and Benjamin, so they’re leaving. They drugged the champagne to erase everyone’s recent memories, and Benjamin asks Janie for her diary. Detective Montclair arrives, but the apothecary gives him champagne too. Janie’s memories fade, as do her parents’ and the detective’s.

The Scotts go home and piece together clues about their life. Sarah tries to talk to Janie about Pip, but Janie doesn’t know who he is. He can’t remember anything either, but he attends St. Beden’s now. The Shiskin family moves to Florida. A year after she returns to the US, Benjamin sends Janie her diary. She recognizes her handwriting and realizes that Benjamin and his father are working to make the world safe.