In a surprising turn of events, Exsedol Folmo is micronized and attempts to seek peace negotiations with the people of the Macross. During the negotiations, Exsedol reveals that the defection of the Zentradi soldiers could be related to a new cultural awakening caused by Minmay's songs. Hikaru begins to long for Misa, who is still on Earth, trying to convince her father and the UN that the two races may have a chance of co-existing peacefully.

Exsedol and Global gather the crew of the Macross to reveal the origin of the nomadic Zentradi at last. Meanwhile, Quamzin's forces attempt to steal a macronization chamber.

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.