Taking place in 2059 A.D., Macross Frontier chronicles the events of the 25th Frontier fleet, located near the center of the Galaxy. The Frontier comes under attack by a mysterious and deadly force of aliens known as the Vajra. Alto Saotome, a young piloting student bored with his life in the colony, joins a special force of Valkyrie pilots formed in order to combat the Vajra.

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.