In the year 2067, eight years after the events in Macross Frontier, a deadly new disease, the "Var Syndrome", threatens the galaxy. The Tactical Music Unit, "Walkure", under the protection of the Valkyrie "Delta Team", join together to combat this new threat. During a Var Syndrome outbreak, the Walkure unit is suddenly attacked by the mysterious "Aerial Knight" Valkyrie Team from the Kingdom of the Wind, the motivation for which remains a mystery...