The episode is interspersed with flashbacks, detailing Simon and River's lives before River's abduction: Simon, a studious young boy, River engaging in flights of imagination while correcting his textbooks, and their father encouraging Simon to become a "brilliant doctor". These expectations are derailed by River's sojourn at an academy, from where she sends letters referring to events which have not happened. The elder Tams are untroubled by River's letters, believing she's just playing games again, and abandon Simon when he takes precipitate and illegal action to rescue her.
In the present day, Simon continues to try to diagnose River's conditions and injuries, while Mal demands that they stay out of the way while he conducts business. On arrival at the backwater colony of Jiangyin, Shepherd Book aids Mal and Jayne in unloading and penning the cattle and meeting with the Grange brothers, their disreputable buyers. Just as they come to an agreement on price, local law enforcement arrives to arrest the clients, and Book is wounded in the ensuing gunfight.
Meanwhile, Simon and River join Inara and Kaylee in town as the women are shopping. Although Kaylee contemplates buying something nice for Simon, the doctor manages to insult her and her beloved Serenity with his complaints about his predicament, and the Tams are left to their own devices. Simon quickly discovers River has wandered off. She finds a country dance, and Simon watches his sister enjoy herself for a change. River's ecstatic dancing suddenly falters when Book is shot, but before Simon can react to his sister's distress, he is kidnapped by a group of men. River follows Simon and his kidnappers, and is seized as well.
Mal and Zoe manage to get Book back to Serenity to perform field surgery and stabilize him. When Wash is unable to find the doctor to help Book, Mal realizes that Simon and River have probably been taken by local hill folk who kidnap unwary people, especially skilled workers. He makes the decision to abandon the Tams in order to get Book off-planet and to proper medical treatment. On Inara's insistence, they seek assistance from the Alliance cruiser Magellan; its captain is ready to dismiss Book's condition until Book offers them his identification card, at which point the captain orders urgent care. Mal and the crew wonder what kind of connection with the Alliance Book must have, but a recovering Book dodges Mal's questions, claiming merely that "it's good to be home."
The hill folk welcome Simon and his sister. When Simon sees the many ill villagers, he settles into his vocation, but continues to insist that they have been kidnapped and should be released. Doralee, the village teacher who runs the infirmary, merely suggests that Simon may well be in the place he is fated to be. Simon and River share a memory of their childhood, and River despairs of how her plight has taken everything Simon had away from him. When River tells Doralee about the cause of a young mute girl's silence, Doralee realizes that River has an unusual power, but assumes this means that River is a witch, and should therefore be burnt at the stake. Simon appeals to the villagers, but when these efforts fail, he instead takes his place next to his sister, prepared to be burned with her. It is at this moment that Serenity swoops over the village, Jayne dangling from its hold with shotgun at the ready, while Mal and Zoe stride in from behind, proclaiming themselves "big damn heroes" (a phrase that has been embraced enthusiastically by the show's fanbase) and demanding the release of the Tams.
As Serenity leaves Jiangyin, Simon asks Mal why he came back for them, and Mal explains off-handedly that Simon is part of his crew. "But you don't even like me," Simon reminds him. "Why'd you do it?" "You're on my crew," Mal repeats. "Why are we still talking about this?" The Tams join the rest of the crew for a cheerful dinner, having found a home.