In the Land of Mages, worth and power are measured by a person's ability to increase crop production. In this agriculturally orientated land, however, dwells a girl named Nimya who dares to dream of something completely different. Nimya desperately wants to build a successful flying machine, and despite the lack of support from her peers, she has dedicated her life to fulfilling her dream. It may take the help of a certain traveler and their motorrad to help bring it to fruition.

Kino and Hermes make their way to the Land of Books, a country whose library gathers together all the books in the world, but locks away those considered ‘harmful', leaving only the most wholesome and inoffensive out on display. Almost by chance, however, Kino finds themselves thrust into the underground of this world, where a secret resistance publishes its own, darker material. But as the plot thickens, the lines between reality and fantasy begin to blur, until it becomes almost impossible to distinguish what is really happening, and what only exists on the pages of a book, or in the depths of an author's mind...

While searching for a village where they can get Hermes' speedometer repaired, Kino stumbles across a family living in the woods, served by an old woman who claims to be a mechanical doll. As she spends time with 'Nanny' and her family, Kino finds themselves impressed by the old woman, but begins to wonder about her origins -- for neither Nanny nor the family seem to be exactly what they claim...

As Kino takes a boat downriver and enjoys a lazy fishing trip, they finds themselves recalling the people they have met on their travels — people who were undertaking journeys of their own, from a woman seeking revenge for her husband's death to another hoping to spread the word of peace. But as Kino recalls their past — and how they chose not to intervene — they cannot help remembering an encounter with a dying wise man that ultimately proved that even observers can have an effect.

Kino and Hermes visit a land that prides itself on a being a peaceful nation, but on entering the country, they soon realize that all is not as it seems. For, while abandoned military equipment litters the streets, on the outskirts of town, an army is training for a war to be held on the following day! Curious as to these contradictions, Kino visits the local museum to find out more about the history of this land, only to discover firsthand that this nation's definition of 'peace' is far more disturbing than they could have envisioned...

When Kino hears of a land where travelers are shunned, they decide to visit anyway and experience the people's attitude for themselves. To their surprise, however, the inhabitants are extremely friendly and welcoming, and Kino is soon made to feel at home among them. And when they make friends with Sakura, a girl who reminds Kino of their younger self, Kino begins to wonder if, for once, they should stay longer than their customary three days.