Zentradi commander Britai Kridanik and his archivist, Exsedol Folmo, begin suspecting that the humans (or 'miclones') are the long-lost 'Protoculture' and send attack waves to test their theory. During a Zentradi attack, Global orders the Macross to "reconfigure" itself to combat mode in order to fend them off. However, the move proves disastrous for the unsuspecting civilians and infrastructure. Roy and Minmay convince Hikaru to join the UN Spacy fleet on the Macross so he could continue flying.

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.

A TV station is launched on the Macross, and to celebrate, the first ever 'Miss Macross' beauty pageant takes place. Minmay enters, but by doing so she ends up missing dinner with Hikaru on the same night. A Zentradi spy ship approaches the Macross and with Max and Kakizaki on leave, Hikaru intercepts it alone.

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.

As the four miclone prisoners attempt to make their escape, a fearsome female Zentradi pilot, Milia Fallyna, attempts to approach the Macross on her Queadluun-Rau powered armor to help sneak aboard the three Zentradi spies - now micronized to human size.

Max encounters Milia in the park and a knife fight between them ensues when she reveals that she is a Zentradi. Max defeats her for the third time, sparing her life, and the two fall in love. Milia decides to join the Macross and their immediate marriage marks the first union between a human and Zentradi, causing celebrations everywhere along Macross City. Boddole Zer, on the other hand, doesn't like the idea and plans to fix the 'contamination' that is human culture once and for all.