The game is set in A.D. 2060, fifty years after the Space War I conflict seen in the first Super Dimension Fortress Macross television series and one year after the Vajra War depicted in the Macross Frontier television series.
Above the planet Ouroboros in the far reaches of the galaxy, Strategic Military Services (S.M.S.) Sephira Branch pilot Leon Sakaki 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.
Due to the intermittent space-fold faults known as "Ouroboros Aurora," Leon cannot immediately return home. He decides to join Aisha in investigating the planet's ruins, and while on an underground survey, the two discover a sleeping girl named Mina Forte. Unknown to them, their fates will be crossed with the ones throughout space and time.
