Q and Raya travel into Raya’s notebook, finding themselves inside one of her songs in a glowing sphere on a vast ocean. Raya realizes that this is the train’s maintenance department, where her songs have been kept alive. She becomes emotional, having believed for years that the songs she wrote before Jace’s death had turned to dust in the abandoned notebook. Q tells Raya that they can’t be sure they’ll survive the night. He says that if he’s going to die, he wants to spend his last moments with a friend rather than with a stranger. He then realizes that a part of them met on this ocean before they ever boarded the train because he has been painting her songs his entire life—meaning that the best parts of them knew each other long before they met.

To continue their “day trip,” Raya has Q write the address of his old art studio in a notebook, creating a portal to that time and place. Inside the studio, Q is overwhelmed by seeing the life he lived while blind. Declaring his old paintings his “disease,” he decides to burn them. Raya stops him and points out that the canvases depict fragments of many different faces, not just one. She discovers a painting of a wrist circled by the name “Lily.” Raya tells Q that he couldn’t remember the face in his dreams because Lily wears many faces. Suddenly, Rasmus calls down to them, announcing that he has finished the barometer.

Back in the Archive, Rasmus demonstrates his barometer, a device that releases laughter-filled balloons into each train car. If the sadness in a car rises, the corresponding balloon bursts, ringing a bell tied to its string. As they help hang the bells, Q tells Raya that he’s relieved to know Lily is the source of his dreams, as he can now thank her for inspiring his art. He mentions a new mystery: He dreamt of Lily’s current face before ever seeing it. Before Rasmus can answer, a bell rings, signaling that sadness is rising in the engine car. Rasmus reveals that the crystal train can’t go there: According to a rare manual, the only entrance is through the ravine at the Dragonfly car, which can be reached only by jumping off the bridge 2,000 feet above it.

At the Dragonfly car, Q and Raya jump through a hole cut in the swaying cobweb bridge. They discover a misprint in the manual as they fall upward, crashing through a painted sky and landing beside a brook. Raya follows the sound of music to a tree and finds a small, lacquered music box in its hollow. The box unfolds on her palm into a miniature mirrored ballroom where porcelain dancers twirl in the pattern of an eternal knot. In the center of the whirling dancers stands a plain black door.

This chapter is a brief excerpt from the Elsewhere Express Operating Manual. It states that the train’s engine is fueled by the wandering thoughts of its passengers and is in constant motion. The only maintenance it requires is peace and quiet, making it the one place on the train reserved for itself.

Q and Raya enter the miniature ballroom and find that the porcelain dancers wear the changing faces of the train’s passengers. To cross the floor to a door at the center, they must move with the dancers. When Q’s clumsiness makes the dancers spin faster, Raya leads him in a dance, telling him to close his eyes and trust her. Guided by her, Q moves gracefully. They step through the door into a quiet living room. Raya feels the wall and proposes that the room is the engine and that the dancers represent the passengers; Q confirms it by touching the wall himself and feeling the engine’s hum. Together, they conclude that the passengers’ precise, choreographed actions keep the train running.

The scent of rain signals the stowaway’s arrival, and Abbie sets a web. A swarm of moths flies into the trap, forming a human-like figure. When the figure’s face is revealed, Raya screams that it’s her brother, Jace. Q sees only the swarm. Raya hears Jace’s voice begging for help, but Q hears nothing and insists that it’s a trick by the stowaway. Raya cuts the stowaway free from the web and shoves it into the crystal train, closing the tiny doors to lock the stowaway inside. Q is briefly relieved, believing that they have averted disaster, but when he sees Raya pick up the crystal train and move it to another track, he shouts that she’s making a mistake. She responds, “No, I’m fixing one” (289).

In Rasmus’s office, Raya explains that she sent the crystal train containing the stowaway to an unknown location, believing that she was saving Jace. Rasmus insists that it was a trick, one the stowaway previously used on Lily. Raya accuses Rasmus of lying, citing his deception about Olly and the Echoes. She realizes that the golden knot on her hand is a leash, not a bond. A bell rings, signaling the stowaway’s new location. To prevent Raya from interfering again, Rasmus has Abbie bind her to a chair with a web.

After Rasmus and Q leave, Lily arrives. Abbie attacks Lily, but Lily stomps on and crushes the mechanical spider. Lily then uses one of Abbie’s severed legs to slash Raya’s binds and free her, stating that her duty as the conductor is to protect passengers. She tells Raya that she can hear the train’s songs beating in Raya’s heart and urges her to listen to them to find a shortcut to the stowaway.

Q and Rasmus are in the supply closet, a car that resembles terraced rice paddies. Rasmus instructs Q to create a magical trap for the stowaway by pulling supplies from the paddies; if he pictures a paintbrush, a rice stalk will become one. Q’s initial attempts fail due to his doubt. Rasmus tells him that he was chosen because he knows how to break rules and must channel his rage to paint a void from which the monster can’t escape. Focusing on his anger, Q successfully pulls a stalk that transforms into a set of black paintbrushes. Rasmus then collapses. He reveals that his tether to Abbie has broken—because Abbie was destroyed—and that the weight of the Archive is crushing him. He gives Q a pouch of seeds to plant, which erupt into a field of lavender. Weakening, Rasmus sends Q to the next car, explaining that the lavender will summon love songs to heal him.

In the Archive, Lily gathers Abbie’s broken pieces. She reflects that some of a conductor’s duties must be performed “in the shadows” and feels a brief pang of guilt for destroying the spider (303). She resolves to use Mr. Goh’s memory-erasing serum to forget the incident later. For now, she puts on her conductor’s cap and focuses on her responsibilities.

Raya follows a faint song to a rotary phone in the Archive, which is a shortcut to the train’s hotel lobby. There, she meets Q, who carries Rasmus’s satchel and informs her that Rasmus was injured when his tether to Abbie broke. Raya tells him that Lily destroyed the spider. At the reception desk, an employee named Isla informs them that their journeys have led them both to the same compartment, but there’s only one key. By morning, they must decide which of them will stay on the train and which will leave. In the elevator, Raya acknowledges the impossible choices ahead of them: Q will try to kill the stowaway, while Raya, who believes that the stowaway is her brother, will do everything she can to save him. Only one of them can stay on the train. Q suggests that they should view their “short story” together as ending there on the elevator and that they should pretend that the two people who exit the elevator are different people. Raya agrees.

The narrative shifts to the perspective of the elevator itself, which observes the unspoken connection between Q and Raya. It describes their silent exchange as a “kiss that never took place” (313)—a moment of mutual understanding, forgiveness, and goodbye conveyed through longing gazes rather than physical touch. The elevator feels a rare pang of sorrow as it dings to announce their arrival, ending the moment.

Raya and Q arrive at their shared compartment as the scent of rain signals the stowaway’s proximity. The room is luxurious, with a grass carpet and a painted starry sky on the ceiling. Raya discovers travel-sized toiletries, including a vial of blue memory-erasing serum. As Q looks in the dresser mirror, he sees a flash of something he can’t identify. Suddenly, the compartment shakes violently. The mirror shatters, revealing a void, and both Raya and Q are thrown through it.

Raya and Q land on the floor of a hospital room that Raya recognizes from a recurring dream, where a bandaged Jace lies in a bed. Raya believes that it’s a real miracle, but Q insists that it can’t be her brother. Rasmus bursts into the room and orders them to step away from the bed.

A flashback details Rasmus’s rescue. After he collapsed, winged songs found him. One song repaired Abbie, while another fetched a phoenix, the train’s healer. The phoenix embraced Rasmus with its healing fire while Abbie curled over his fading heart, becoming his new mechanical heart in the process.

In the present, Rasmus explains that the figure in the bed isn’t Jace but the train’s first stowaway, trapped there long ago by him and Lily. Another flashback reveals that a younger Lily was once convinced that this stowaway was the ghost of a friend. During their confrontation, Lily plunged a knife into the stowaway’s back; the stowaway broke apart into moths, and the blade went through the swarm and struck Rasmus’s eye. A sad song, attempting to heal the conflict, instead “fixed” the stowaway by merging with it, engulfing it in the song’s message—“live, breathe, be” (326)—and transforming it into the physical embodiment of the song’s mournful subject: Jace, bandaged in his hospital bed. Unable to discard the being that had saved them, they built a new compartment over the hospital room to imprison both the song and the stowaway. They then erased their own memories of the event.

Raya touches the bandaged figure and recognizes the song she wrote for Jace’s funeral, realizing that the monster is merely wearing her brother’s song like skin. Rasmus explains that the compartment is a prison made of dark thoughts, which cracked when Q’s perceptive gaze glimpsed it through the mirror. Q finds a moth wing, confirming that the second stowaway was there but fled. They agree that the first stowaway must be destroyed. Q channels his darkest emotions and paints a swarm of burnt moths, which come to life and consume the figure and the hospital room, restoring the original compartment. To defeat the second stowaway, Raya determines that she needs a special song and her old guitar, which is in the Missed and Misplaced Department. Rasmus gives her the key.

In the cloakroom, a loudspeaker summons Raya and Q to the boarding car, signaling that the stowaway has been located. Insisting that she needs her guitar first, Raya uses a magical raincoat as a door to the Missed and Misplaced Department. Inside, the stowaway appears, first with Jace’s face and then Q’s, and destroys her guitar. Olly’s spirit intervenes, holding off the creature long enough for Raya to escape. Back in the cloakroom, Q paints a square on the floor opening to a void, and they drop the raincoat—containing the only door to the Missed and Misplaced Department—into it, believing that the stowaway is now trapped in the Missed and Misplaced Department forever. As they embrace in relief, moths burst from the floor, grabbing Raya and dragging her into the void.

Q wakes in Rasmus’s office to learn that Raya is gone. Rasmus reveals that Lily’s summons was a trap for Q, who she believes brought the second stowaway aboard. A flashback confirms that Lily told Rasmus that she knows Q is responsible. When a bell rings, signaling Raya’s location, Rasmus refuses to help, intending to decouple the car to destroy the stowaway and sacrifice Raya. He offers Q a memory-erasing tonic. Q refuses and threatens to use his painting abilities to destroy the entire train unless Rasmus helps him save her. Rasmus relents. Before leaving, Q writes a note, seals it in an envelope, and entrusts it to Rasmus.

Raya now exists as a disembodied consciousness, her thoughts scattered and imprisoned within the individual moths of the stowaway’s swarm. The swarm has taken shelter from a storm inside the hollow of the large oak tree in the boarding car. From her fragmented prison, Raya sees Lily approach with a torch lit with blue flame. Lily calls for Q to show himself.

Q steps out from behind the oak tree to confront Lily. After a tense truce, she reveals her true plan: The boarding car itself is a trap for the stowaway. Using a key, she transforms the meadow into a sealed, decaying room where the stowaway is revealed, holding an unconscious Raya. Lily tells Q that he brought the stowaway onto the train with his darkness and that the only way to save Raya is for him to jump off, as the creature will follow him. When Q hesitates, the stowaway seals Raya in a cocoon of vines.

Trusting his sense of touch over his sight, Q shoves his hand into the swarm of moths. The insects wordlessly communicate a secret truth to him. Understanding what he must do, Q smiles at the thought of Raya having a future on the train and throws himself out through the door he had painted on the wall, falling from the train.

A loudspeaker announcement is made to the passengers of the Elsewhere Express. It states that the cloakroom and the boarding car are now closed and inaccessible for renovations. Due to this closure, the animals that were kept in the boarding car have been displaced. Passengers are informed that these animals are now in need of new homes and that anyone interested in adopting one should contact Mr. Nakamura.