Set in 2059, five decades after the Space War I conflict seen in the first Macross story. Macross Frontier, the 25th New Macross Class super-long-distance colonization fleet, is journeying through the galaxy to a new paradise to call home. However, it is locked in a state of war with a strange enemy called Vajra. Ozma Lee, the leader of the S.M.S. Skull Team that is fighting the Vajra on the frontlines, encounters a mysterious lifeform, different from even the Vajra, one day. This mysterious lifeform leaves an archival video of the Macross 7 colonization fleet with Ozma, Ranka, and Sheryl.