The story is set in the ninth century and gives a fictionalized account of the creation of the Book of Kells, an illuminated manuscript and known today as one of Ireland's greatest national treasures. Obsessed with building a mighty wall to keep marauding Viking raiders from destroying the Abbey of Kells, Abbot Cellach expects his young nephew Brendan to follow in his footsteps. Brendan has apprenticed in the scriptorium of the monastery and has heard the story of Aidan of Iona, a master illuminator who is working on the Book of Iona. Later, Aidan himself comes to the monastery, accompanied by his cat Pangur Bán. Brother Aidan has escaped from the Vikings who have destroyed his own monastery, and had brought the unfinished Book of Iona with him. Taking Brendan under his wing, Aidan asks Brendan to venture into the forest to look for gall nuts to make ink, though the boy is fearful as he was forbidden to go into the forest by his uncle. Brendan eventually decides to venture into the forest, where he meets a forest spirit named Aisling. She is suspicious of Brendan at first, but soon befriends him after helping him find the gall nuts. Though Cellach learns of his adventure and forbids him from leaving the abbey's confines, Brendan secretly defies it as Aidan teaches him illumination while Aisling introduces him to a wider world.
Eventually, Brendan learns that Aidan needs his help to finish Book of Iona due to his failing eyes and hands. However, Aidan finds that a special lens he possessed was lost when he left Iona: the Eye of Collum-Cille. Aidan reveals that his predecessor obtained it from Crom Cruach, a Celtic pagan deity, with whom Brendan had a frightful encounter prior. When Brendan tries to sneak out of the abbey to go to Crom's cave to obtain the other eye, he is caught and confined to his room by Cellach, who later gets into an disagreement with Aidan and demands that he leave when spring arrives. Having overheard the disagreement, Pangur Bán ventures into the forest to get Aisling's help. Aisling frees Brendan, using her magic to turn Pangur Bán into a spirit that retrieves the key to his room, and together they flee into the forest. When Brendan tells Aisling of his plan, she pleads with him not to go through with it, revealing to him that Crom Cruach killed her people and her mother and will surely kill him as well. Brendan tells her that if he doesn't try to get the eye, he can never complete the book. Eventually Aisling agrees to help him and manages to get Brendan into the cave, but appears to be consumed by Crom's darkness in the process. After some struggling, Brendan defeats Crom by taking the god's remaining eye and imprisoning him in a circle of chalk where the blinded Crom consumes himself. With the eye in his possession, he exits the cave to find the cloak he had given to Aisling neatly folded amongst the cracked rock she had lifted to give him entrance inside. Leading away from the spot is a trail of flowers left by Aisling as a sign she survived. With a brief smile, Brendan goes back to the Abbey and continues to help Aidan in secret.
Shortly thereafter, the Vikings arrive and Cellach locks his nephew and Aidan in the scriptorium as his plan to protect everyone from the invaders falls apart. Managing to escape the carnage, Brendan and Aidan are confronted in the woods by the Viking leader and a band of his men. The Viking leader scatters the pages of the book, and the Vikings raise their swords in preparation to strike the two helpless travelers. Before the Vikings can strike Brendan and Aiden down, Aisling's black wolves converge upon them, killing the Vikings. As Brendan and Aiden collect the pages of the book, Aisling, in the form of the white wolf, appears to Brendan, having saved his life yet again before disappearing back into the forest. Brendan and Aiden continued to travel across Ireland, finishing the Book of Iona over the years. Inheriting the book after Aidan's passing, a now adult Brendan ends up back in the forest of his youth where he again meets wolf-Aisling, and she guides him to the village. It turned out only the villagers who made it to the abbey tower survived, along with a guilt-ridden Cellach. We find out Cellach loved Brendan dearly and even speaks to Brother Tang of him as "our most important treasure." Now near death, Cellach finally reunites with the nephew he thought had perished in the massacre long ago, and is able to see the completed Book of Kells. The film closes with a beautiful set of scenes showing the now completed illuminated pages which come to life as viewed.