An abandoned alien battle fortress crash-lands on Earth in 1999, stopping a world war in the process. The international scientific community spends the next ten years reconstructing the damaged ship, called the SDF-1. At the ship's launch in 2009, a race of giant alien warriors, the Zentraedi, appear and attack Earth in a bid to capture the vessel. Young sport pilot Rick Hunter has his first experience with a rather odd fighter plane.

The SDF-1 successfully flies off Macross Island to link up with other Earth forces in orbit. A Zentraedi ambush forces SDF-1 skipper Captain Gloval to go back to Macross Island and attempt a hyperspace jump. The consequences of the jump turn out to be totally unexpected. Meanwhile, Rick tries to bring Minmei back to her family, but crashland in a section of the SDF-1.