The story begins in 1999: a giant alien spacecraft crash-lands on South Atalia Island. Humanity proceeds to attempt to rebuild this marvel, but political conflicts centered around the Macross - coupled with proposals for a one-world government - result in a global war. After 10 years, the 'Unification Wars' are finally over, the new United Nations government is in power, with the UN Spacy as their military arm.

It's 2009: The work on the Macross is now complete. On the day of launching ceremony, its main cannon fires on its own, destroying an alien spacecraft in orbit. This automatic action marks the beginning of the war between the humans and Zentraedi, a race of humanoid warriors of gigantic size.

Air racer and stunt pilot Hikaru Ichijo and his 'sempai' (mentor) Major Roy Fokker attempt a daring rescue mission when South Atalia Island is invaded and bombarded by Zentradi forces. Hikaru has his first encounter with Lynn Minmay, a young waitress, as Zentradi mecha begin raiding the city. Meanwhile, Captain Bruno J. Global, Lieutenant Misa Hayase, Bridge Operator Claudia LaSalle, and the crew of the Macross attempt to launch the ship for the first time.