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.

Flash Back 2012 is Minmay's farewell concert. Featuring some of her best songs, the music is performed over various scenes and events taken from the first Macross television series as well as Macross: Do You Remember Love film. Also included is a newly animated closing sequence showing the launch of Misa's colony vessel, the Megaroad-01, into space.

Three decades after the great war between the humans and the Zentradi, the U.N. government is developing new technologies to use in their transforming fighter aircraft by running tests on the colony planet Eden. Military test pilots and former childhood friends, loose cannon Isamu Alva Dyson and the Zentradi mixed race Guld Goa Bowman, are selected to each pilot a new aircraft (Shinsei Industries' YF-19 & General Galaxy's YF-21) for Project Super Nova, to choose the newest successor to the VF-11 Thunderbolt variable fighter which is currently still in use by the U.N. Spacy military forces. Their own personal grudges end up disrupting the tests, and begin to wreak havoc on the program.

Basara, on one of his frequent trips across the galaxy to spread the message of his music, folds in on an icy planet. The natives are hostile, and take him prisoner until he begins to sing for them and a little boy named Pedro recognizes his voice. They release Basara, and almost as soon as they don, a strange wailing voice comes from the nearby mountains. Basara and Pedro head out in Basara's valkyrie to investigate the noise. Little do they know, an ambush is waiting for them.

Plot Summary: A.D. 2089 - 80 years have passed since Space War I changed the lives of both human and Zentraedi races. Both races are at peace on Earth when a new alien race called the "Marduk" appear within the Solar System. While covering the first battle between the U.N. Spacy and the Marduk fleet, SNN rookie reporter Hibiki Kanzaki discovers Ishtar, an "Emulator" that enhances the Marduk's combat abilities through singing. Hibiki brings Ishtar to Earth to teach her the values of life and culture. Together with ace Valkyrie pilot Silvie Gena, Hibiki and Ishtar must find a way to save Earth from total destruction at the hands of the Marduk leader Ingues.