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.

With Hikaru still reeling from the horrors he's witnessed first hand from both sides, events take a turn for the worst when the space folding system of the Macross (a faster-than-light travel technology) teleports it and the city on South Atalia Island to the edge of the Solar system and in front of Pluto.