Jin Lo strides purposefully away from the bunker, looking like a young man in a hard hat and jumpsuit, and she boards a bus, followed by the invisible children. Jin Lo explains that she knows Burrows only through the exchange of letters; she was an apprentice to a chemist in Shanghai. By the time they disembark, all three are again visible and wearing stolen clothing. They go to the apothecary shop, though Benjamin and Janie can’t remember any more about the night the Scar broke in. Jin Lo mixes up some herbs and oils and then smears the mixture on Janie’s and Benjamin’s wrists and temples. She tells them to grasp her wrists, and she takes theirs, encouraging them to remember. Janie begins to feel dizzy, and the present falls away. She recalls hearing the apothecary tell Benjamin that he’d be “in the shelter” (190), something she didn’t recall earlier. Benjamin explains that his father uses an old Morrison shelter as a table, but when Janie looks back at Jin Lo, she can tell that the woman is remembering her own past. Janie carefully wipes the oil from the woman’s wrists, and Jin Lo returns to the present. They open the shelter, and Jin Lo points to a small pile of salt, calling it “Lot’s wife.” She explains that this pile of salt is, in fact, Benjamin’s father.

Jin Lo gathers every grain of salt and pours them into a clean beaker. Jin Lo asks where Burrows’s real lab is, and Janie suggests that it’s behind the locked door in the cellar. Once they get in, Jin Lo mixes up a big pot of goo and adds the salt, but not before Benjamin has a sentimental moment with the beaker. She stretches the goo with a spoon, and Janie spots a knee, then an arm, then a head, and finally, Burrows’s entire body emerges from the pot, covered in the potion.

Benjamin hugs his father fiercely, and Jin Lo introduces herself to the surprised apothecary. Janie introduces Pip, and Jin Lo assures Burrows that he didn’t miss the test since the boat leaves tomorrow. Burrows wants to go to the physic garden, but Janie tells him that the gardener is dead. Just then, they hear footsteps upstairs. They sneak quietly up the ladder, and Janie recognizes Danby and the Scar. As the Scar lunges for her, Jin Lo blows some gray powder in their faces, temporarily blinding them.

Janie tells Mrs. Parrish that she’s spending the night at her friend Sarah’s to do their Latin homework. Benjamin tells Jin Lo and Burrows that Danby is a double agent, and Burrows is astounded to learn that the children tried the avian elixir. They decide to hide under the garden’s white mulberry tree until morning, and the children assure Burrows that the Pharmacopoeia is safely hidden at the school.

Burrows explains that the work of apothecaries and alchemists accelerates during wartime because so many need healing. He recounts the events of World War II and describes the Cold War arms race that followed it. He wanted to find a way to contain the damage that these bombs could cause and has been working to this end. Jin Lo has developed a kind of net that turns into polymer when it comes in contact with radiation, and as the polymer contracts, it contains the explosion. Burrows is to contribute something that will absorb the radiation within the polymer, and he landed on the “Quintessence” created by the jaival tree’s flower.

He describes the Quintessence as the fifth element and the “source of all life. A life force to combat a killing force” (212). The physic garden contains a jaival tree, but Burrows must force it to bloom so that he can harvest its flowers. Shiskin told Burrows that the Soviets planned to test a new bomb in the north, and Jin Lo and Count Vilmos, a Hungarian physicist, came to London for this reason. Benjamin and Janie realize that this is who they saw in the hotel. Burrows says that Vilmos, or “Vili,” found a way to freeze time, slowing it down around him while he moves at normal speed. That night, they sleep in the garden, and Benjamin shares his jacket with Janie.

Jin Lo and Burrows dig holes around the jaival tree and fill them with powder, liquid, and dirt; suddenly, green leaves and white buds form. When the flowers are fully grown, Burrows harvests several. Thick black smoke rises from the tree, and it rumbles as though expressing disapproval. Burrows says that the Pharmacopoeia calls this the “Dark Force,” but he has never seen it form in this way. The children want to go with him to Russia, but Burrows refuses. However, he does need the Pharmacopoeia.

In two hours, Burrows and Jin Lo are supposed to meet Count Vili at the icebreaker ship called the Kong Olaf. They reach St. Beden’s and find the Pharmacopoeia where they hid it, among other books in the chemistry lab. They run into Sergei, and he tells them that the MGB, a Soviet security force, kidnapped his mother and sister and will kill them unless his father helps the Soviets take the boat. Benjamin, Janie, and Pip are determined to get on it, and Pip suggests that they ask Sarah for heavy clothes that are appropriate for the voyage. In addition, he also convinces Sarah to give up her gold necklace so that they can make more invisibility elixir, telling her that it’s a project for their science team.

Benjamin, Pip, Janie, and Sarah all go to Sarah’s house. She finds them heavy coats and boots to wear on their expedition to Russia, and the butler offers to have a trunk delivered to the ship. This is perfect because the children plan to be invisible when they board.

The chauffeur returns Sarah to St. Beden’s and drives the other three to the port. They meet Vili, and he introduces them to Captain Norberg, explaining that they can speak freely because the crew knows the plan. They deliver the Pharmacopoeia to Burrows, and Janie begs him to let them accompany him, believing that this is what she’d say if they didn’t have a plan to sneak onboard later. He forces them to leave the boat.

Pip looks in nearby homes to choose one that is unoccupied. He finds one and picks the lock, and they slip inside. They run a bath, but a neighbor knocks on the door. Pip claims that he’s the resident’s nephew and turns her away. Meanwhile, Benjamin and Janie pour the invisibility serum into the water and take turns submerging themselves, but Janie accidentally removes the drain plug, and most of the water runs out before Pip can take his turn. He says that he’ll find another way onto the boat. When they go outside, they see a car containing Danby, the Scar, and Shiskin. They overhear Shiskin saying that he doesn’t want to help Danby and the Soviets because the apothecary is his friend, and he asks why Danby cares so much about Russia. Danby explains that he studied there and fell in love with the citizens’ pride, unlike the more reticent English. He also believes that the Soviets can keep the US’s growing power in check.

Janie asks Benjamin if he still wants to be a spy or if he wants to be an apothecary now, but he doesn’t see much difference between the two at this point. Detective Montclair and Officer O’Nan arrive, looking for the children, as they’ve been reported truant and were spotted on the boat. Vili claims that the children who were there earlier had been out fishing with him all day, but Montclair doesn’t buy it. Pip tells Janie to get ready and then shows himself, taking off through the crowd as though he hadn’t noticed the police before. When they chase Pip, Janie and Benjamin have a clear path up the gangway.

Benjamin and Janie sneak into the storage room containing Sarah’s trunk, and they can hear Shiskin outside. Shortly thereafter, Jin Lo bursts in with a gun, and they tell her that Shiskin is there to double-cross Burrows and the team. Jin Lo breaks into Shiskin’s room and threatens to kill him, but he says that he must send a message every six hours or else his comrades will know he has been captured. They tie him up and take his wooden leg so that he can’t escape. The children explain everything to Burrows, who feels that they must update Captain Norberg.