On board the battlefortress, Lisa, Rick, Max, and Ben relate their experience and observations as prisoners of the alien invaders to their superior officers. There are promotions all around, and their exploits are cause for celebration among the civilians and soldiers of Macross City. Rick is briefly reunited with Lynn Minmei, who has become quite a star, a virtual singing sensation. He can’t help but feel that hey are growing apart. The three Zentraedi spies observe the festivities with all the enthusiasm of children in a huge toy store. They are beginning to enjoy the Micronian culture.

The Zentraedi commanders are eager to learn more about the Micronian culture and investigate their knowledge of protoculture. Rico, Bron and Konda volunteer to be reduced to Micronian size so that they may infiltrate the SDF-1 and report their findings to Breetai and Dolza.

While performing their mission, Lisa, Rick, and Ben are captured by the Zentraedi. Max Sterling managed to escape. They are interrogated by Breetai, Exedore, and Dolza, the supreme commander of the Zentraedi armada. In the course of the questioning, the Zentraedi officials demand that the Micronians tell them what they know about protoculture – something the humans protest they have never heard of. The Zentraedi want to learn about Micronian customs and are shocked to learn that human children are born from a female parent. Rick and Lisa provide an example of the affection humans demonstrate for each other by kissing. The Zentraedi are so shocked that they have the prisoners removed to other quarters.

Ordered to fire a warning shot across the bow of the SDF-1, Khyron takes matters into his own hands again. The blast knocks out the radar tower of the giant spacefortress. The stress of constant battle has already taken its toll on the SDF-1, and much of the sophisticated electronic equipment no longer functions properly. The aliens make contact with Captain Gloval, demanding the ship’s surrender. Gloval retaliates by planning a new defense.

The citizens of Macross City hold a beauty contest to boost morale among soldiers and civilians alike. Lynn Minmei is one of twenty eight eager and attractive contestants chosen from nearly four hundred applicants. Minmei's charismatic charm has already made her the darling of the SDF-1. She wins the title of Miss Macross hands down and becomes the official Queen of the City.

As Minmei prepares for her sixteenth birthday, the SDF-1 continues to orbit Mars. Operating on auxiliary power, the battlefortress is under a constant barrage of fire from alien ships and battle pods. With its main engines damaged and the fold system inoperative, the SDF-1 is unable to escape. Khyron and his Zentraedi troops press their advantage at every turn, despite Breetai’s orders to the contrary. The commander wants to capture the ship intact.

Emerging from hyperspace above Mars, Breetai sets an ambush for the SDF-1. He also calls up for reinforcement – the 7th Mechanized Division of the Botoru Fleet. Exedore is alarmed at this turn of events. The Botoru division is commanded by Khyron, a ruthless Zentraedi warlord who has earned himself the nickname “Backstabber”. Khyron’s motto is victory at all costs – even at the unnecessary risk of his own men. Breetai agrees that Khyron’s measures are extreme at best, but so far, the warlord’s division has remained undefeated. Breetai cannot afford to lose the SDF-1.

In its new configuration, the SDF-1 is able to repel the attacking Zentraedi forces, although at great cost to Macross City. The modular transformation destroys much of the city, due to the radical effects on the fortress’s basic structure. In the months that follow, the citizens pull together and repair the damage. Once again, they try to lead normal lives.

Despite the incredible disruption in their lives, the citizens of Macross City make the best of their situation. Reunited with her aunt and uncle at their restaurant, Lynn Minmei persuades them to reopen. The first Chinese restaurant in space – and Minmei – prove to be very popular with the inhabitants of the SDF-1.

While the bridge crew of the SDF-1 plans its next course of action, Rick Hunter tries a maneuver of his own. Initially trapped in the vacuum of space outside the battlefortress when the SDF-1 executed the fold, Rick and Minmei enter an unexplored area of the ship. With the radio broken, they have no way to call for help. Although Roy Fokker quickly determines that his friend is missing, he is ordered to assist in retrieving the surviving 70,000 civilians of Macross Island. The two young people are left to their own resources.

Lieutenant Commander Fokker returns to bring Hunter and Minmei to the safety of the SDF-1. Captain Gloval tries to determine the Zentraedi strategy while Breetai puzzles over how to capture the SDF-1 with the least amount of damage. Exedore warns his commander that, once free of the planet’s gravity, the ship can execute a hyperspace fold that will carry them beyond the reach of Zentraedi weapons. Breetai reluctantly increases the laser bombardment.

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Aboard the SDF-1, Vanessa reports to Captain Gloval that twenty-four unidentified objects are touching down just offshore. Gloval asks why they weren't detected earlier, and Vanessa tells him the energy drain from the firing of the main gun knocked out their radar. "Those scout ships were just a decoy," Gloval muses. "Very clever strategy." He asks Lisa to recall Lt. Comm. Fokker's forces, but with the Veritechs still busy fighting off the first wave, Gloval instead orders the carrier Prometheus to send out reconnaissance choppers. Lisa says she's already called for them, and they should arrive in five minutes.