Brendan, a young, curious, and idealistic boy living in the tightly knit community at the Monastery of Kells, is under the strict care of his stern uncle, Abbot Cellach. Cellach is obsessed with building a wall around the Abbey of Kells, in order to prevent Viking attacks.
Brendan is apprenticed in the scriptorium of the monastery. After listening to the other monks of the monastery talk about Brother Aidan, the creator of the Book of Iona, Brendan is curious about the mysterious illuminator and “the book that turns darkness into light” (the unfinished Book of Kells). Aidan arrives in Kells, accompanied by his white cat, Pangur Bán, after his own monastery is destroyed by a raid. After eavesdropping on a discussion between Cellach and Aidan, Brendan wanders to the scriptorium, where he finds the still-to-be-completed book. Pangur Bán guards the book, but when the cat sees that Brendan means no harm to the book, she accepts him. Aidan arrives and tells Brendan about the book.
Seeing Brendan as a suitable apprentice, Aidan sends Brendan, with Pangur Bán for company, into the woods to obtain gall nuts to make ink for the illumination of the book. However, Brendan is cornered by a hungry pack of wolves. He is saved by Aisling, the forest spirit from the beginning of the film. Although at first suspicious of Brendan’s presence, Aisling slowly comes to accept him after he reveals his intentions of helping to create the book.
After a brief yet scary close encounter with Crom Cruach, a deity of death and destruction, of whom Aisling is deeply afraid, Brendan and Aisling return to the outskirts of the forest. She assures Brendan that he can come back and visit anytime he wants.
Upon his return home, Brendan is reprimanded by Cellach, who forbids him to leave the monastery again. However, Brendan continues to work with Aidan. Brendan learns that Aidan’s work is endangered by the loss of the Eye of Colm Cille, a special magnifying lens captured from Crom Cruach. When Brendan tries to leave to visit Crom’s cave to obtain another Eye, he is confined to his room by Cellach.
Pangur Bán and Aisling set Brendan free. After running into the heart of the woods, Brendan tells Aisling of his objective. A shocked Aisling begs him not to confront the dark deity, warning that Crom Cruach will kill him just as it killed the rest of her people. But Brendan persuades Aisling to assist him, by stating that if he does not retrieve the Eye, the book will never be completed. Convinced, Aisling helps Brendan enter Crom’s cave, nearly getting killed in the process. Brendan duels with Crom and seizes the Eye, blinding Crom and causing the dark deity to consume itself, becoming an ouroboros. Upon returning to the cave entrance, Brendan finds the forest covered in white flowers.
Brendan returns to the abbey and continues to assists Aidan in secret. The brothers of the monastery excitedly watch the two create the book. In a fit of frustration, Cellach locks Brendan and Aidan in the scriptorium, but not before ripping out a page that Brendan had created for the book. Shortly thereafter, the Vikings invade Kells, and Cellach watches in horror as they breach the wooden gate. Brendan and Aidan manage to escape by using smoke from the gall berry ink, confusing the raiders when they burst into the scriptorium.
Cellach is stabbed by a Viking raider; Brendan is dragged away by the frantic Aidan, who tells him that there is nothing that he can do. After they leave, Cellach, having survived the attack, sees the burning remains of the scriptorium. Thinking that his nephew has perished, Cellach falls into a deep despair.
While running through the woods, Brendan and Aidan are confronted by the raiders, and the Viking leader takes the book’s bejeweled cover and scatters the pages. Before two Viking raiders can kill Brendan and Aidan, Aisling’s black wolves attack the Vikings, saving the two refugees. Brendan and Aidan gather the pages and depart. Cellach and the remaining villagers take refuge in the monastery.
Brendan and Aidan travel across Ireland, and, after many years, complete the book. Aidan, after entrusting the book to Brendan, dies. The now-adult Brendan returns to Kells with Pangur Bán, guided by Aisling (in wolf form). The guilt-ridden Cellach is nearing death. Brendan and the abbot happily reunite, and Brendan displays the complete Book of Kells to his uncle. The film closes with an animation rendition of some of the illuminated pages of the book.