The game is set in year 2060, 50 years after the Space War I conflict seen in the first Macross series and one year after the Vajra War seen in Macross Frontier. Above the planet Ouroboros in the far reaches of the galaxy, S.M.S. pilot Leon Sagaki is suddenly attacked by an unknown enemy and shot down in his YF-25 Prophecy. There, he is rescued by the heroine Aisha Blanchette, the young Zentradi head of S.M.S.'s branch on Ouroboros.