The launch ceremony for the rebuilt alien space battleship Macross is interrupted by the arrival of the alien Zentradi forces as well as a booby trap in the Macross itself. A civilian pilot named Hikaru Ichijo is drawn into the conflict.
The Captain of the Macross is forced to make a quick decision due to the relentless attackes of the enemy. Using alien technology, the Macross makes a space fold near the Earth's surface above South Ataria island.
Having discovered an abandoned base on Mars, the Zentradi set up a trap for the Macross. The Macross, already far off the intended course for Earth, makes a stop on Mars for much needed supplies.
Roli, Konda, and Warera, after having all their recording equipment destroyed by Hikaru, report to Britai and Exedol about the broadcast they witnessed.
Hikaru regains consciousness but is being kept in the hospital for monitoring. His first visitor is Misa, who feels guilty for being responsible for Hikaru's injuries.
After the attack on the city inside the Macross, the civilians get to work cleaning up. Meanwhile, the military is kept busy fighting off small groups of Zentradi.
Misa decides to return to the Earth to give her report to the UN Government High Command regarding the Zentradi, using data obtained from the defectors.
Two years have gone by since the battle with Boddole Zer. an the Macross is now in a conflict called the Space War I. Hikaru asks Roy what he should do about his romantic feelings for Minmay and Misa.