The game is preceded by a 30-minute audio drama. It describes an age when humans tried again to dominate nature, and the Guild of Weavers became known for weaving influence into reality as well as cloth. Persecuted for this, they bought an island called Loom.

Lady Cygna Threadbare begs the Elders of the Guild of Weavers to use the Loom to end the suffering of the Weavers, whose numbers are failing and whose seed is barren. The Elders refuse, but Cygna secretly uses the Loom and draws an infant from it. She gives the child to Dame Hetchel, and the Elders transform Cygna into a swan and banish her.

The child, Bobbin, grows up ostracized and is not allowed to learn the ways of the Guild until his seventeenth birthday. Hetchel secretly teaches him some basics of weaving, and the game begins on the day he is summoned to learn his fate.

At the Sanctuary, Bobbin sees Hetchel punished for teaching him, then watches the Elders and the villagers transformed into swans by a visiting swan. Left alone, he frees Hetchel and learns that the swan has come to save the Weavers from the Third Shadow. He then sets out, meets other guilds, and later faces Bishop Mandible, who seeks powerful relics and unleashes Chaos.