One night, a boy named Takuto washes up on shore swimming from the mainland. He later enrolls in Southern Cross High School as a freshman and makes new friends. However, beneath the school is a group of mysterious giants called Cybodies, which can be controlled by humans in an alternate dimension known as Zero Time. Takuto, The "Galactic Pretty Boy", finds himself dragged into opposition with the "Glittering Crux Brigade".

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.

Олівер, молодий священик, залишає церкву, щоб перевірити стародавню легенду і вирушає у подорож на острів «G» - володіння злого бога Гештальта. Це небезпечне заборонене місце, звідки ніхто не повертався. По випадковості у нього з'являється попутниця - німа дівчина Орі, чия справжня натура розкриється трохи згодом.