35 years have passed since Lynn Minmay had brought peace between the Zentradi and the humans in the events of Macross. Nekki Basara is a guitarist and a singer of the band Fire Bomber. Living in a less-developed part of the flying colony City 7 which is looking for a habitable planet, he composes and sings songs in the belief that music holds a greater power. During its flight, an unknown alien race appeared and started laying siege upon City 7. However, its attacks are not conventional -- instead of trying to destroy them, they steal what is known as "spiritia", rendering victims unresponsive and zombie-like. During these battles, Basara always goes out into the middle of the warzone, singing his songs and expecting friend and foe to listen and be moved by his music.

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