As Rick, Ben, Max and Lisa are debriefed about their experience aboard the Zentradi flagship, the micronized spies Rico, Bron and Konda awkwardly attempt to participate in Micronian society. Meanwhile, the SDF-1 breaks through the quarreling forces of Khyron and Azonia to splashdown on Earth.

With his ship safely returned to Earth, Captain Gloval recaps the role of the SDF-1 in the Robotech War in a report to the United Earth Government. With the story told, Gloval recognizes that his crew has only scratched the surface regarding the secrets of Robotechnology.

In light of the Earth government's insistence that the people of Macross stay aboard the SDF-1, a mere two aircraft leave the battle fortress for vastly different reasons. The first carries Captain Henry Gloval and First Officer Lisa Hayes to the Earth Government's military headquarters in the Alaskan wilderness where the SDF-1's commanding officers plead with the top brass (including Lisa's father) to allow the ship's civilians to disembark. Gloval and Hayes are shocked to learn that the crew and civilians of the SDF-1 are pawns in a plot of smug Admirals to keep the public from learning about the war occurring in outer space. They order the ship to depart again still carrying the civilians. Aboard the other aircraft, Rick Hunter carries Lynn Minmei on a special visa to visit her parents in Japan. Once there, they encounter Minmei's cousin, Lynn Kyle, an avowed pacifist with great disdain for the military who returns to the SDF-1 with Rick and Minmei.

The simultaneous arrival of Lynn Kyle and the announcement that the Macross civilians will be taken back into space creates hostility between the civilians and members of the military. Though Kyle professes non-violence, he uses his extraordinary martial arts skills to stop a brawl in his parent's restaurant. Shortly thereafter, Khyron once again leads an unauthorized attack on the battle fortress. Driven literally to distraction by the similarities between Kyle and her late fiancée Karl Riber, Lisa mistakenly orders a missile launch that catches Rick in the crossfire. The unconscious Lieutenant Hunter is retrieved and rushed to a hospital in the city.

Recovering from serious injuries incurred during Khyron's attack, Rick's delirious mind attempts to make sense of his life. He imagines that Zentradi Lord Breetai has kidnapped Minmei and attempts to rescue her by joining the Defense Forces. Humiliated in his rescue attempts time and again, Rick turns to Lisa, Max and Ben for help and succeeds in reaching Minmei. Once there, Rick learns it is not Breetai holding Minmei hostage, but a fifty-foot tall Lynn Kyle. Rick defeats Kyle, but realizes his position with Minmei will remain tenuous until she chooses between Rick and her career.

In hopes of cheering up his little brother, Roy Fokker arranges for Minmei to visit Rick in the hospital. When Minmei finally arrives, she is exhausted and falls asleep in Rick's bed, providing little comfort to the wounded pilot. Suddenly, the war once again intrudes forcefully into Rick's life as Myria, ace pilot of the Zentradi, bursts into the skies above Macross in dogged pursuit of Max Sterling's Veritech. Though Max succeeds in chasing off his pursuer, Roy Fokker is fatally injured in the course of the battle. The news of Fokker's death rattles the ship. Communications officer Claudia Grant has lost her fiancée, and Rick Hunter has lost his closest friend.