Fire Emblem Genealogy of the Holy War is a custom English Translated game. It takes place on the continent of Judgral, which is divided between eight countries: the Kingdom of Grannvale, the Kingdom of Verdane, the Dominion of Agustria, the Republic of Manster, the Kingdom of Thracia, the Republic of Miletos, the Kingdom of Silesse, and the Kingdom of Isaach. According to staff, Judgral is within the same world as Archanea, the continent featured in the original Fire Emblem and its sequels: the events of Genealogy of the Holy War are set hundreds of years prior to the time period of Archanea, with the latter being in a barely civilized state. It was during this time time that the Dragon Tribes were debating how to treat humanity. In ancient times in the year Grann 440, the Earth Dragon Loptyr made a pact with the priest Galle, who becomes his vessel for bringing ruin to humanity. By 632, the Divine Dragon Naga had discovered Loptyr's part in the gradual conquest of Judgral, so she chose twelve soldiers to defeat Loptyr: this event became known as the Miracle of Darna. The Twelve Crusaders defeated Loptyr and his cult, bringing peace to the land in a conflict dubbed the "Holy War" — these twelve would go on to establish Judgral's countries. The events of Genealogy of the Holy War begin in the year 757.
During the opening, Grannvale is at war with the kingdom of Isaach, in response to Rivough barbarians besieging Darna Castle. Sigurd, a loyal Lord of Grannvale, rides out to aid allies in another part of Grannvale. In the course of fighting, he gathers several allies, some of whom are descendants of the Twelve Crusaders. During his invasion of Verdane, and running into Isaachian princess Ayra and prince Shanan, he meets a mysterious girl named Deirdre. She is revealed to be of Naga blood, a long-lost member of the Grannvalian royal family, and the descendant of the crusader with the power to defeat Loptyr. Sigurd and Deirdre fall in love and marry, and their son Seliph is born in Agustria. At this point, an alliance of Grannvale dukes stage an attempt to seize the throne, murdering the Grannvalian prince Kurth and framing Sigurd and his father for the crime. Sigurd is forced into exile, while the archbishop Manfroy of the Loptyr Sect kidnaps Deirdre and erases her memories in order to use her to resurrect Loptyr. His plan is to wed her to Lord Arvis of Velthomer marry - the two are, unbeknownst to them, siblings, and their union will produce a human vessel capable of hosting the consciousness of Loptyr. During their exile, Sigurd and his allies are forced to hide their children from the forces of Arvis and the Loptyr cult. After a year in exile, Sigurd begins making his way back through Judgrel, killing the Dukes responsible for the false accusation. Apparently forgiven, Sigurd returns to Grannvale, only to learn that Arvis has married Dierdre to become Grannvale's king before being killed with his party by a magical attack.
Over the next fifteen years, Grannvale expands to hold dominion over the whole of Judgral, with Arvis becoming Grannvale's emperor. His and Dierdre's son Julius is successfully corrupted by Manfroy and becomes Loptyr's host - Dierdre sacrifices herself to protect her second child Julia, who had inherited the Naga bloodline. At this point, Sigurd's son Seliph comes out of hiding to protect a nearby village, revealing his long-hidden existence to Grannvale. Traveling across the lands of Judgrel, Seliph reunites with the long-hidden children of Sigurd's companions, along with Julia. Making his way through the countries of Jugdrel, he gains support from the surviving powers, and gradually frees Grannvale's conquered territories. Arvis is powerless to prevent Julius from taking over the Empire, and is killed in battle against Seliph after an unsuccessful attempt to subvert his son's rule. During the course of these battles, Julia is captured and Manfroy and Julius attempt to sacrifice her as her powers could banish Loptyr for good. Seliph manages to save her, and after defeating Julius in battle, Julia successfully banishes Loptyr, ending his rule for good and allowing Judgrel to recover from the recent conflicts.