Less than a year after the events of the Macross 7 TV series, Basara departs from Fire Bomber and journeys to the planet Zola. There, he encounters a girl named Elma, an ardent admirer of Fire Bomber. On this planet, he is compelled to wield his Spiritia abilities once more, this time to prevent a band of poachers and Elma's father Graham from slaughtering a pod of space whales migrating through the planetary system.

In this installment

After a devastating conflict with the Zentradi, a powerful alien race, humanity set out toward the galactic core using a fleet of colony vessels collectively called the Macross Frontier. As the alien menace seemed to recede, life on the ships returned to a normal routine by the year 2059. Alto Saotome, an aspiring mecha pilot, and his fellow cadets were assigned to provide backup for famous singer Sheryl Nome during her concert aboard the Macross Frontier. The show was abruptly disrupted when the Vajra, a biomechanical alien species, appeared. The Vajra breached the ship's defenses and crash-landed near the concert area, triggering chaos. In the ensuing panic, a young girl named Ranka Lee became trapped and was targeted by the Vajra, but Alto managed to rescue her just in time. Following these incidents, the Strategic Military Services recognized Alto's remarkable combat skills and recruited him to fight this new extraterrestrial threat.