The war that raged between the Church and the Witches for five centuries finally ended in peace but a few short years ago. However, nestled in the shadowy places of the world, the embers of that age old conflict still smoulder.

Attending the Royal Academy of Magic of the Kingdom of Wenias is a struggling student named Sable, who has no memories of his time before being enrolled. At the command of Headmaster Albus, he left the Kingdom to travel to the southern reaches of the continent, where anti-magic insurgents are still a force to be reckoned with, as part of a special training regimen. Accompanying him are a party of individuals strong in both ability and personality; there's the one known as the Witch of the Dawn, Roux Cristasse, who seeks the forbidden knowledge of primeval magic in the 'Grimoire of Zero', the genius girl Holtz, as well as the school's sole beast, Kudd.

Just what truth shall they uncover in their journey to the south…?

Macross Delta is set in the year 2067, eight years after the events of Macross Frontier in a remote part of the Milky Way Galaxy called the Brísingr Globular Cluster, which is plagued by the Var Syndrome, a mysterious phenomenon which turns people berserk without any apparent cause. A team of talented idols, the Walkure, uses the power of their songs to calm down the infected by the Var Syndrome, assisted by the Delta Flight, a team of experienced Valkyrie pilots. At the same time they are facing the interference from the Aerial Knights of the Windermere Kingdom, which found a way to exploit the infection in their favor as part of their plan to resume war against the New United Government for control of the Cluster.