The crew of the Macross are informed to not let anyone, including civilians, leave the ship, so as to keep the truth of the Zentradi's existence from causing widespread panic. The civilians within the Macross become increasingly unruly and violent toward the military personnel and crew members. Meanwhile, Quamzin returns, breaking orders and attacking the Macross while it sits in the Atlantic ocean.

Milia is now aboard the Macross as a spy and marvels at human culture. The premiere of Minmay's film Shao Pi Long (Little White Dragon) takes place. A Zentradi attack prompts another transformation to combat mode, and Hikaru and Misa end up being trapped within the walls of the ship, where they end up learning more about each other. Milia continues to search for the miclone pilot who defeated her.

The battle within the city comes to a close, with the surviving Zentradi defectors coming to terms with the destruction they caused. Along with Rori, Konda and Warera, the defectors are all given asylum within the Macross. Misa prepares to travel back to Earth to the UN Headquarters, whilst Hikaru begins to further contemplate his feelings for her.