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.

With the fold systems now vanished, Captain Global and his crew come to a realization that the Macross must make a long journey back to Earth. The civilians from South Atalia Island - along with their shops and homes - are brought onto the ship. Meanwhile, Hikaru and Minmay are trapped within the confines of the Macross. Hikaru learns much about Minmay and begins a new friendship with her.

Using a defensive anomaly left behind after the disappearance of the fold systems, and the rings of Saturn to hide the Macross, Misa and Claudia devise a new attack strategy against the Zentradi.

After being captured by the Zentradi, Misa, Hikaru and Kakizaki are 'interviewed' on human culture by Britai, Exsedol, and Supreme Commander of all Zentradi forces, Golg Boddole Zer - marking the first verbal encounter between the two races. They discover that the Zentradi have no sense of culture and fear intimacy between men and women. Max, having been separated from the others, formulates a plan to rescue them. Meanwhile, Minmay begins a singing career on the Macross.

Whilst Misa and Global travel to the Alaskan headquarters of the new UN, Hikaru escorts Minmay to Japan so that she could visit her parents. Lynn Kaifun, a relative of Minmay, joins the Macross to see his parents and protect Minmay.

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Max has a chance encounter with Milia in a video game arcade, and proceeds to defeating her a second time during a game. They arrange to have a date in the park later, where Milia secretly plans to destroy him. Misa is escorted back to Earth by Hikaru, so that she could meet her father.