It is A.D. 2009 and the human race is caught in a war between giant humanoids, male Zentrans and female Meltrans. Returning from the edge of our solar system after making a space fold, the SDF-1 Macross makes the long journey back to Earth with survivors of South Ataria Island.

Picking up from where the previous movie left off, Ranka's star career flourishes while Sheryl's health rapidly deteriorates after collapsing during a live performance. At the same time, separate factions are maneuvering behind the scenes seeking to control the Vajra horde by utilizing the singing abilities of the two songstresses. As the entire Macross Frontier fleet begins to wage its final war on the Vajra, Alto finally makes a choice between Ranka and Sheryl.