One year has passed since the events of Mobile Suit Gundam Unicorn and the Laplace's Box was opened. Following the conflict called the "Laplace Incident", the Neo Zeon remnant force known as the Sleeves is destroyed. Both the Banshee and Unicorn Gundam are sealed away from public consciousness, locked in secrecy and meant to be forgotten by history. However, sightings of another Gundam are suddenly being reported. The Unicorn Gundam 03 Phenex, thought to be lost since two years ago, has reappeared.

In the land of Iolph, all the people stop aging in their mid-teens and can live for hundreds of years. One resident, Maquia, feels lonely despite the peaceful and idyllic land she lives in. But one day, the Mesarte army invades Iolph, seeking the peoples' blood for their immortality. Maquia manages to escape the destruction and chaos of war, but with no home or people, she becomes a wanderer in a dark forest. She comes across Erial, an infant mortal boy who has lost his parents, and becomes his guardian. The story follows the relationship that evolves between the two as Erial grows up while Maquia does not.