Music idol Sheryl Nome arrives at the Macross Frontier fleet for a concert performance. In the meantime, fleet command deals with an unidentified & powerful alien enemy.

Overwhelmed by the new enemies' speed & power (despite their lesser numbers), fleet defenses cannot prevent some of the alien bio mecha from penetrating the main colony ship. Teenage music fan Ranka Lee, young student Saotome Alto & S.M.S. VF-25 veteran pilot Ozma Lee are all involved in the ordeal.

Ranka Lee is on her way to S.M.S. to drop off some items for her older brother Ozma Lee when she happens to meet Sheryl Nome. Alto Saotome also shows up when the two arrive at an observation park, but then the Vajra loom over from the skies above.

After the Macross Galaxy fleet is hit by a large-scale Vajra attack, Alto Saotome and his unit head out in the S.M.S. Macross 25 warship to rescue the surviving ships. On the same day Sheryl gives her last live concert on Macross Frontier.

The secret of "Aimo", the lullaby that only Ranka and Brera know is finally revealed.

While Sheryl is recovering from her illness, all her work is cancelled. When she is informed that Ranka's popularity is now rising she becomes insecure and worried about her own musical career. During that time, Alto and Ranka give her a friendly visit.

At Ranka's concert in Mihoshi Academy Ranka, Alto and Sheryl meet. While their thoughts and feelings cross each other during the event, the Vajra attack and Ranka's group becomes caught in a very dangerous and deadly situation.

In the on-going war against the Vajra, people lose their loved ones and their hatred grows. Refusing to be a singing tool and wanting to clear up other people's thoughts, Ranka is determined to take a major step.

After arriving at the planet of origin of the Vajra, the Frontier fleet commences an all-out attack and Battle Frontier manages to charge directly into the center of the enemy forces. However, Island One (the main residential area of the fleet) receives a fierce counterattack from the Vajra and becomes endangered. During that time of crisis, the silhouette of a person starts projecting on the stage at the Battle 25 bridge.