The Scott family relocates from Los Angeles to London to avoid being forced to testify about friends accused of communism.

Janie and her father visit the neighborhood apothecary shop, where the friendly owner offers her powders to ease her homesickness.

Benjamin Burrows boldly refuses to participate in a school bomb drill at lunch, immediately catching Janie's admiration.

Benjamin takes Janie to Hyde Park to spy on Shiskin, and they follow a well-dressed man to a hotel where a clerk calls him 'your excellency.'

Marcus Burrows burns papers in his shop, forces the Pharmacopoeia on Benjamin, and hides the children in the cellar as German-speaking intruders ransack the shop.

At the Chelsea Physic Garden, the elderly gardener explains the Pharmacopoeia's origins and tells the children about Jin Lo, a Chinese chemist.

The children return to the physic garden and find the gardener mortally wounded; he tells them to run and points them to a hidden bottle.

On the roof of Turnbull Hall, Benjamin, Janie, and Pip drink the avian elixir and transform into birds to escape Danby.

The invisible children enter the secret bunker and discover the prisoner is Jin Lo, not Mr. Burrows; Pip picks her restraints to free her.

Jin Lo mixes a large pot of goo using every grain of salt from the Morrison shelter, and Marcus Burrows emerges from it fully restored.

Hiding under the physic garden's mulberry tree, Burrows reveals his plan to use the Quintessence and Jin Lo's polymer net to contain a Soviet bomb.

Burrows forces the jaival tree to bloom and harvests its flowers while thick black smoke, the Dark Force, rises from the tree in apparent disapproval.

Watching from a Soviet ship's deck, Janie sees the bomb detonate and then witnesses its mushroom cloud contract back on itself, confirming the plan worked.

The Dark Force overtakes the helicopter carrying Janie, Benjamin, Danby, and the Scar, sending Janie and Benjamin plunging into the Arctic sea.

At a train station farewell, Burrows drugs everyone's champagne to erase their memories of recent events, and the Burrowses board a train out of England.

After their family is forced to flee the American Red Scare, Janie and her parents arrive in a gray, bomb-scarred London that feels nothing like home. When the local apothecary's shop is ransacked by German-speaking men and Mr. Burrows vanishes, his son Benjamin and Janie are thrust into a dangerous mission to find him. Following a trail of magical clues from the Chelsea Physic Garden to a secret government bunker, the children discover that Burrows has been transformed into a pile of salt and must be restored by the Chinese chemist Jin Lo. The reunited group races to Nova Zembla to stop a Soviet bomb test using an ancient remedy, the Quintessence, combined with Jin Lo's polymer net, and their plan ultimately succeeds when Janie watches the mushroom cloud contract from a ship deck. After a harrowing escape from the Arctic sea, the apothecary drugs everyone's champagne at a train station farewell, erasing all memory of the adventure to protect those he loves.

The core adventure from London arrival to erased memories.

Janie notices a black sedan tailing her home from school and narrowly manages to lose it before reaching her apartment.

On her first day at St. Beden's, Sarah Pennington escorts Janie to Mr. Danby's Latin class and explains he was a Royal Air Force pilot and prisoner of war.

Benjamin catches up with Janie after school, tells her he wants to be a spy, and asks her to meet him at school on Saturday.

Janie visits her parents on the Sherwood Forest television set at Riverton Studios and finds her homesickness beginning to ease.

On a Sunday in Hyde Park, Mr. Burrows unexpectedly sits beside Shiskin, picks up his newspaper, and his entire face darkens with alarm.

Benjamin and Janie test the veritas herb on each other; Benjamin involuntarily admits he likes Sarah, and Janie admits she likes Benjamin.

At the Shiskins' flat, the veritas brew spills and everyone inhales it; Shiskin is forced to reveal that Burrows is to meet him at a ship in two days.

With her parents away for work, Janie lets Benjamin climb through her window, and together they examine the gardener's note and the mysterious bottle.

Detained at Turnbull Hall, Janie and Benjamin meet Pip, a streetwise pickpocket and housebreaker who immediately offers to help them escape.

In the chemistry lab, the children brew the invisibility serum; Janie sacrifices her late grandmother's gold earrings to supply the required gold.

The three invisible children slip into a bunker elevator alongside Danby and a British general, overhearing that their prisoner hasn't yet spoken.

After Burrows is restored, Danby and the Scar arrive at the apothecary shop; Jin Lo blinds them with gray powder and the group slips away.

Sergei tells the children that Soviet agents kidnapped his mother and sister and will kill them unless his father helps the Soviets seize the ship.

At the Port of London, Pip boldly runs from Detective Montclair to create a diversion while invisible Benjamin and Janie slip up the gangway.

A full year after losing her memory, Janie receives a package in the mail containing her red diary and a note from Benjamin saying the world is safer now.

Before the grand mission begins, a series of smaller but essential events lay the groundwork: Janie is followed home, meets her key allies at school, and gets her first glimpse of the spy world through Benjamin's Saturday park surveillance. The children gather intelligence through cunning experiments with the veritas herb, and a quiet night examining the gardener's hidden bottle marks the point of no return. Their arrest and detention at Turnbull Hall introduces Pip, whose streetwise skills prove indispensable throughout the rest of the story. The group's preparations—making the invisibility serum, recruiting Sarah, and securing supplies—show the careful teamwork required before they can act. By the story's quiet coda, after all memories have been stripped away, a package arriving in the mail a full year later restores Janie's past to her one page at a time.

Quieter but vital moments that shaped the adventure.

At a family dinner, Janie's father explains the government is persecuting innocent people over communism; a furious Janie blames her parents for uprooting her life.

Benjamin recognizes the Pharmacopoeia's symbol from somewhere else and leads Janie to the Chelsea Physic Garden, where they find it engraved on a locked gate.

After the veritas herb forces him to answer the children's questions, Shiskin swallows a muting pill that immediately silences him completely.

Hoping he can help translate the Pharmacopoeia, Janie tells Mr. Danby about the book and the apothecary's disappearance, a decision that infuriates Benjamin.

Police officers arrive at lunch to take Benjamin and Janie; Benjamin quickly slides his satchel containing the Pharmacopoeia to Sergei's feet just before they are seized.

The children recognize the scarred man behind Danby's steering wheel and realize in an instant that their trusted teacher is not their ally.

Three birds follow Danby's car across London to a hidden bunker, then resume human form outside and devise a plan to sneak inside using invisibility.

The moment Pip lays eyes on Sarah Pennington outside the chess club at St. Beden's, he falls instantly and completely in love with her.

Jin Lo applies the oil of Mnemosyne to Janie's and Benjamin's wrists at the apothecary shop, unlocking a memory about Burrows saying he would be in the shelter.

Jin Lo points to a small pile of salt inside the Morrison shelter and reveals it is Marcus Burrows, who transformed himself to hide from the intruders.

Shiskin presses a gun to Janie's head aboard the ship; Count Vili freezes time, wrenches her free, and takes Shiskin's weapon before anyone else can move.

Aboard the renamed ship, Benjamin confesses to Janie that he no longer likes Sarah and that he now likes Janie; they share their first kiss.

The Scar catches Janie inside the bomb facility on Nova Zembla, and Danby coldly decides to leave her on deck so the bomb's radiation will kill her.

In the freezing Arctic water, Janie refuses to leave the barely conscious Benjamin and save herself; Hirra reaches into the sea and pulls them both to safety.

The Scotts return home unable to remember anything; Sarah tries to discuss Pip with Janie, but Janie has no idea who he is.

The story pivots repeatedly on moments of sudden revelation and courageous choice, beginning when Janie's father explains the Red Scare and Janie must confront her own anger at her parents. Trust is tested and broken when the children realize that Mr. Danby—a teacher they admired—is a double agent, and rebuilt when unexpected allies like Pip and Vili prove their loyalty at critical moments. The apothecary's true nature unfolds in a sequence of shocking discoveries: a memory-unlocking oil reveals where Burrows hid, and a pile of salt turns out to be the man himself. On the ship and at the bomb site, time freezes, mushroom clouds contract, and two young people fall in love amid crisis, each moment reshaping who they are. The story closes not with triumph but with absence—a blank where memories used to be—until a diary arrives and finally makes the impossible real again.