The Delta Conflict happens around the period of IS 3405 although historians are still looking into the exact years. It lasted over a period of 13 months.

Kooluk, an empire disbanded during IS 400 grows back into power from the tension of two opposite factions. The Patriarchal Faction desires to bring Kooluk back to his former glory of Kingdom while his counterpart, the Matriarchal Faction dreams of a Queendom. The Patriarchs aware of the recently ended civil war in Gordius launch an invasion, hoping to get the men's support by force after a series of failed diplomacy attempts. The Matriachs see this as a threat and they request aid from the Alma Kinan in the north and the Mermaid from the south. This results in a war between genders.

Hero from Masculine War and his Mannequin bear Masculine and Feminine Rune after the civil war. Gordius' central cathedral collapsed and the city is in turmoil. Before anything can return to normal Gordius is attacked by Kooluk Patriarchs and the Matriarchs, slipping through the chaos manage to steal the Feminine Rune and put Mannequin into a coma. Gordius comes with a truce with the Patriarchs to defeat the Matriarchs and Hero lend his Masculine Rune to the Patriarchs. 

Hero II is a high ranking officer of the Patriarchs who is after an ambush from the Matriarchs, witness the last moments of his superior, whom the Masculine Rune is lend to. He lands a vinishing blow to the women superior and as the two gender rune bearers dead, the runes got transferred into him, a new host. The Royal spies frame him for treasons to both sides and he is now a wanted men from both the Patriarchs and Matriarchs as well as the Royal. 

As a bearer of two runes, he is constantly on a run with a couple of his friends from the Patriarchs. The group travels west, passing the Moon Village and seeks refuge in The East. 

Hero II realizes that the war will not be over unless the Royal is stopped. The East Emperor aids him in defeating the Kooluk.

The conflict ends with the Patriarchs and their supporters move into The Southeast while leaving the Kooluk area to the Matriarchs. The Royal Kooluk is killed, ending the royal blood of the empire. The conflict does give birth to the third division of the Gender Rune. The Masculine Rune is returned to Hero I and Feminine Rune to his Mannequin while the third rune goes missing. It eventually leads to the third war in the region, The Mini War.