The plot of "Maquia" follows the entirety of a human life through the eyes of an immortal. After finding the infant Ariel, Maquia raises him as her own. As Ariel grows, he becomes a teenager and feels alienated by Maquia's unchanging age, leading to a temporary rift between them. He joins the army of Mezarte, the very kingdom that destroyed his mother's home, and marries his childhood friend, Dita. During a climactic battle, Mezarte is defeated. Maquia helps Dita give birth to their child while Ariel is wounded in the fighting. They share a heartfelt reunion and farewell before Maquia leaves to help her friend Leilia escape the fallen kingdom.
Leilia, who was forced to bear a child for the royal family, is reunited with her daughter, Medmel, for only a moment before choosing to leave her behind, flying away with Maquia on the last Renato. The ending of the film features a significant time jump of about forty years. Maquia returns to visit an elderly, dying Ariel. In a profoundly emotional scene, she holds his hand as he passes away, finally allowing herself to cry as she remembers their life together. The film concludes with Maquia acknowledging that despite the deep pain of loss, loving Ariel brought her true happiness. A post-credits scene shows the Iorph's village being rebuilt, with their descendants, implying a future for their people and that Maquia will continue to live on and form new bonds.