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.
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.
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.