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.

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.

After a few months of fighting, the Macross arrives at Mars. Detecting an abandoned base on the planet's surface, the crew land the ship to gather much needed supplies. Quamzin Kravshera, a brilliant but unstable Zentradi commander, attacks the Macross. Meanwhile, Misa requests permission to investigate an emergency signal from within the base.

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.

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.

As some of the giant Zentradi begin to rebel over their new way of life with the humans, Minmay's fame begins to slip away. Wandering around from tour to tour of the local towns, Minmay contemplates at what could have been a serious relationship with the now distant Hikaru.

Global informs Misa that the SDF-2, the successor to the Macross, is nearly ready to begin colonizing the galaxy - with her as the captain of the mission. Now that the reaction engine is built into his craft, Quazmin, Laplamiz, and their henchmen attack Macross City with missiles and waves of mecha. Hikaru, Misa and Minmay's love triangle reaches its climax, as Hikaru must decide whether he will go with the pop idol who brushed him aside and now desperately needs him, or the military commander who loves him deeply, but may leave him forever by the line of duty.