In 1999, a city-sized alien spacecraft crashes in South Ataria Island on Earth. Over the course of 10 years the military organization
U.N. Spacy reverse-engineers its technology and rebuilds the spacecraft, naming it the SDF-1
Macross. In 2009 at the launch ceremony of the
Macross, a young civilian pilot,
Hikaru Ichijyo, comes to visit the
Macross upon U.N. Spacy pilot
Roy Föcker's request. During the launch ceremony, a space war fleet from an alien race of
humanoid giants arrives in the
Solar System and identifies the
Macross as a former battleship used by their enemies, the Supervision Army. As the aliens, known as the
Zentradi, approach the
Macross, the original systems override the crew's commands and fire its main cannon, wiping out the advance alien scouts and starting a war. While Hikaru takes the new
VF-1 Valkyrie on a test flight, the aliens retaliate. He then encounters
Lynn Minmay and rescues her from the aliens. The
Macross crew attempts to use the experimental "
Fold System" (
faster-than-light drives) to escape to the Moon's orbit, but instead it accidentally takes the
Macross and South Ataria Island to the edge of the solar system. The people from the
Macross salvage everything they can, including the city surrounding the ship and its civilians (who have survived in special safety shelters, which were transported along intact), and attach two aircraft carriers to the ship. Since the fold systems have vanished after the jump, the
Macross is forced to make its way back to Earth by conventional power. The Zentradi suspect the humans might be their creators, the Protoculture. Under the command of
Britai Kridanik and
Exsedol Folmo, they plot ways to understand them. Fearful of their old combat directives of not interfering with Protoculture, the Zentradi perform attacks to test their theories about the people on board the
Macross, and even have their Zentradi soldiers "micloned" (miniaturized) to learn more about their culture. The Zentradi capture several
Macross personnel, including Officer
Misa Hayase and Hikaru, to study.
Boddole Zer, Supreme Commander of the Zentradi, is puzzled over things such as relationships amongst males and females. He confirms that the Miclones "are" Protoculture during a demonstrated kiss between Hayase and Hikaru. After escaping, Hikaru and the others report their findings to their superiors, who have trouble accepting the reasons behind the Zentradi attacks as well as the huge forces the aliens possess. After much difficulty returning to Earth, the UN Spacy refuses to allow the
Macross and the civilian passengers to return to land. Minmay's cousin, Lynn Kaifun, decides to join the
Macross to see his parents and also look after Minmay. Because of Kaifun's relationship and constant contact with Minmay, the pair eventually enter a romantic relationship. After deliberation, the UN Spacy orders the
Macross to leave Earth as a means to get the Zentradi away from them. During these events, a female Zentradi ace fighter pilot,
Milia Fallyna, is micloned and attempts to assassinate
Maximilian Jenius, an ace UN Spacy pilot. Attempting to kill him during a knife duel, Milia is defeated and falls in love with Max, and the two are subsequently married. Their wedding aboard the
Macross is broadcast to the Zentradi as a message that aliens and humans can co-exist. Since the Zentradi's exposure to culture and to Lynn Minmay's songs, some of them become eager to join the humans. Believing the "miclone contamination" is becoming a threat to all Zentradi forces, Boddole Zer orders his entire army to exterminate the human race and all those Zentradi previously exposed to human culture. Because
Britai Kridanik was "contaminated" as well, he works with the humans to defeat the main Zentradi forces. The resulting battle culminates in the large scale devastation of Earth, but the people of the SDF-1 survive. After Boddole Zer is killed and his armada defeated, the surviving humans and their Zentradi allies begin rebuilding Earth. Two years after the end of the first Space War, the transition into the Human ways becomes difficult to some Zentradi who cannot stand the idea of a pacified life.
Quamzin Kravshera constantly incites conflicts towards the civilians. He repairs a damaged Zentradi warship to return to his old ways and attacks the new Macross City built around the SDF-1. Moments before the final Zentradi attack, Misa Hayase tells Hikaru Ichijyo of her feelings for him and her decision to leave to space in a colonization mission to preserve human culture across the galaxy. Lynn Minmay, who was left by Kaifun and now loves Hikaru, does not want him to leave to join the fight. However, Hikaru still goes to defend the city anyway. Eventually Quamzin is killed. After a long emotional conflict Hikaru finally decides to be with Misa and join the colonization mission, but the two remain good friends with Minmay in the end. ==Production==