Macross Delta is set in the year 2067, eight years after the events of Macross Frontier. The story focuses on Walküre, a team of talented idols and the Delta Squadron, a team of experienced Valkyrie pilots as they battle against the Var Syndrome, a mysterious phenomena that is consuming the galaxy, alongside the mysterious Aerial Knights Valkyrie fighter team of the Kingdom of Wind. This film recompiles scenes from the television anime with new scenes to tell a different story.

Walküre and Delta Flight used music to save people from the Vár Syndrome, a previously unknown disease that made humans and others go berserk. However, they find themselves facing a new threat.