In a post-war alternative timeline, Japan is divided into the North, controlled by the Union, and the South, controlled by the United States. A mysterious high tower rises within the borders of the Union. Three high school students promise to cross the border with a self-built airplane and unravel the secret of the tower.

Taking place one year before the events of the original Macross series, Macross Zero chronicles the final days of the war between the U.N. Spacy and anti-U.N. factions. After being shot down by the anti-U.N.'s newest fighter plane, ace pilot Shin Kudo finds himself on the remote island of Mayan, where technology is almost non-existent....