Agate Fluorite is the new transfer student at the elite school, "Cluster E.A.", in which the sons of many prestigious families from different countries gather to study together. Soon after, Agate's unexpected antics and enthusiasm in life impress many of his schoolmates, including Beryl Jasper, an honor student who is bored with his current way of life. However, unknown to Agate, he was born with a secret power that can create.
Taking place one year before the Zentraedi arrive on Earth, 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 tranqulity of the island is shattered by a battle that involves the UN's newest fighter - the VF-0.