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. While Shin stays on the island to heal his wounds, the tranquility of the island is shattered by a battle that involves the UN's newest fighter - the VF-0.

In a vast and mysterious multiverse with fantastic alternative realities, a metaphysical entity has a whole plan behind it, in order to protect the timeline of an island using a book that can see the past, present and future as if it were a full script.