Benjamin knows where the Shiskins live. When Sergei answers the door, Benjamin and Janie say that they want him to be the third member of their science team, which is conducting an experiment to determine the properties of an herb; they explain that they must brew it. Sergei says that his mother and sister are in Russia, and he shows them his family’s samovar. Sergei’s father enters, and when they tell him that they’re doing an “experiment,” he narrows his eyes.

They boil the veritas leaves and offer the brew to Shiskin to smell, but Benjamin covers his nose, and this makes the man suspicious. Benjamin says that they got the plant in the park, but Shiskin orders him to smell it and then answer again. Shiskin realizes that the children created this ruse to “get to” him, and Benjamin accidentally drops the samovar. The water spills everywhere, and everyone smells it. Janie admits that the plant came from the physic garden, and Shiskin realizes that he saw them at the park.

Benjamin admits that Marcus Burrows is his father, and Shiskin asks if they saw a man with a scar when Burrows was taken. This scarred man is a member of the Stasi, the East German secret police. Shiskin grudgingly reveals that Burrows is supposed to meet him on a ship at the Port of London in two days. When Benjamin asks about their plan, Shiskin takes a pill that temporarily but completely eliminates his ability to speak.

The children return to the garden to warn the gardener since Shiskin said they were all in danger. The gardener is in his cabin and has been stabbed with the sundial. Barely alive, he tells them to avoid the police and run but to “allow for the possibilities” (91). He hid a small bottle hidden under the veritas plant in the garden, and Janie finds it. She pockets it, and they run.

Benjamin and Janie run to her flat, and the Scotts are furious with her for being so late. Benjamin admits that he doesn’t know where his father is, and Janie’s parents want to call the police. The children insist that they shouldn’t, and when Benjamin refuses to provide more information, Davis orders him to leave and Janie to go to bed. Janie is writing in her diary when she hears a tap at the window; it’s Benjamin. He notes the existence of Janie’s diary and lies down on her floor. He crawls under the bed when Davis comes to the door, and Janie’s father tells her that their boss wants them to go shoot on location. They want her to come with them, but Janie says she’s too far behind in school already. Her parents agree that she can check in with Mrs. Parrish, the landlady, if she promises to be safe.

After he leaves, Benjamin and Janie look at the bottle, which is wrapped in a note. The gardener wrote that the man with the scar came to the garden and that the children must find Benjamin’s father. The bottle contains the avian elixir, which he made according to the Pharmacopoeia’s directions. Benjamin still doubts the efficacy of such a concoction due to the physical laws of nature. Eventually, they fall asleep.

When Janie awakens, Benjamin is gone. He left a note saying that he’d see her at school. Janie’s school uniform arrives in the mail, and Marjorie gives her a safety pin for the too-big skirt. Janie promises her parents that she’ll check in with Mrs. Parrish while they’re gone.

At school, Mr. Danby gives Janie a couple Henry James paperbacks, and she gazes into his “kind” eyes, thinking that he could have been a movie star. He asks if everything is okay, and Janie decides to tell him a little about what’s going on, hoping that he can help translate the Pharmacopoeia, which is partly in Latin. He wants her to go to the police but seems willing to help with the text. Benjamin is furious when she tells him that she told Danby.

That day, at lunch, a police officer and detective come to collect Janie and Benjamin. They try to run, but the police officer tackles Benjamin, who slides his satchel with the Pharmacopoeia to Sergei’s feet. Sergei picks it up and walks away. The detective drives Benjamin and Janie to Turnbull Juvenile Court for questioning.

Turnbull Hall looks like it’s straight out of a Charles Dickens novel: derelict and grubby. Detective Montclair questions Janie and accuses her parents of being communists. He suggests that she has no alibi for the time when the gardener was killed. Afraid to contradict whatever Benjamin might say, Janie stays quiet. Officer O’Nan escorts her to a cell near the one in which Benjamin and another boy sit. Benjamin introduces her to Pip, a pickpocket and housebreaker. Pip asks if Janie has a hairpin that he can use to pick the lock, and she gives him a safety pin.

Just then, Danby enters, and the matron declares that he’s from the Foreign Office. Benjamin is delighted that their teacher is a spy, and Danby offers to take them for hot cocoa. He says that he was assigned to St. Beden’s to look for “emerging—talent” and to keep an eye on Benjamin in particular. When they reach Danby’s car, they realize that the man with the scar is his driver.

The children realize that Danby isn’t their friend and run back inside the hall. They tell the matron that he’s a Soviet spy, but she doesn’t believe them. Benjamin and Janie ask a group of children how to escape, and they release Pip and make a run for the kitchen door. When Danby enters the room, they climb up to the roof, and Janie suggests that they use the avian elixir to escape. Danby follows and tries to convince them to come down. The children run to the top of the turret while Danby pursues them, insisting that he isn’t a Russian spy. Benjamin drinks a bit of the elixir, and his body begins to change.

Benjamin turns into a skylark, and Pip changes into a swallow. Janie drinks, and she feels her body changing shape into a red-breasted robin. She leaps from the roof as Danby snatches her scarf, though when she fully transforms, she realizes that she’s missing feathers around her shoulders. The three birds soar, following the car containing Danby and “the Scar.”

When the car stops, the children—still birds—hear them discussing what happened. Danby knows that they don’t trust him anymore and laments the “muting pills” taken by their prisoner, whom the children assume must be Burrows. The men go inside a building, and the children resume their human shapes. Pip says that the men went into a secret bunker, and they discuss how to get inside unseen. Janie suggests that they make themselves invisible, but they’ll need the Pharmacopoeia first.

The children reach St. Beden’s just as school is letting out. The moment Pip sees Sarah Pennington, he falls instantly in love, and she seems taken with him too. When Janie says that Benjamin also likes her, Benjamin denies it, saying that he “used to” like her. They find Sergei at the chess club, and he returns the book. Meanwhile, Pip soundly beats another boy at chess and demands payment for their wager. Sergei identifies Pip’s strategy as the “Opera game,” won in 16 moves, and Pip says that his uncle taught him to play in the pub. He tricked the other boy into thinking he couldn’t play. Sergei begs to go with them, but they promised his father that they’d leave him out of it.

They go to the chemistry lab and find the directions they need. For the recipe, they must have about a quarter ounce of melted gold, and Pip points out Janie’s gold earrings. They were her grandmother’s, and she doesn’t really want to give them up. Then, she realizes that her fun-loving grandmother would want them to find Benjamin’s father, so she hands them over. Benjamin translates further, realizing that they must pour the potion into a bath and then get in, naked. They fill a clean garbage can with water and pour in the potion, and then Pip pulls a rolling chalkboard in front of it for modesty. Benjamin leaves out a shoulder, as the book says to leave one body part unaffected, and Pip disrobes next, leaving one ear visible. Janie goes last, leaving one pinky finger dry. Once they’re all invisible, they empty the garbage can and run outside into the chilly air.