The story takes place in 2092, 80 years after the events depicted in Macross: Do You Remember Love? The SDF-1 Macross still exists, as does the U.N. Spacy Minmay Attack stratagem, which has been successfully employed to thwart the Zentradi threat ever since. However, a new humanoid alien race called the Marduk (Mardook in the original Japanese version), arrives in the Solar System with enslaved Zentradi and Meltlandi warriors who are seemingly unaffected by the Minmay Attack. The Marduk employ their own female singers, called Emulators, who incite their giant warriors with songs.
The story focuses on reporter Hibiki Kanzaki, who is caught in the middle of the action when he rescues an Emulator, Ishtar, while covering a battle between the U.N. Spacy and the Marduk. Hibiki proceeds to teach her about Earth's culture, which she then shares with the rest of the Marduk. However, the Marduk leader, Emperor Ingues, considers Earth's culture anathema. With the help of ace fighter pilot Silvie Gena, Hibiki and Ishtar attempt to end the war.