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.

Alto Saotome is put through the paces by Mikhail Buran and the others at S.M.S. Meanwhile, Ranka Lee has passed the initial rounds of the Miss Macross contest auditions and sings a song for the very final screening stage.

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.

Sheryl gives a consolation concert at planet Galia 4, but because of an undisclosed illness she cancels her concert, which causes a huge riot.

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.

Ranka's pet Ai-kun suddenly disappears. Ranka asks Brera for help and they look for Ai-kun together. Along the way, Brera asks Ranka who does she sing for? Ranka, who's beginning to feel doubt about her singing, starts to consider her true feelings. Meanwhile, Sheryl tells Alto that she will no longer sing.

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.

The Frontier populance's hatred of the Vajra is growing by leaps and bounds, and even Alto and Luka cannot control their own hate. Moreover, now armed with new prototype weapons, Alto and Luka consider using them to utterly exterminate all Vajra. However, Ozma (who has been researching Leon's conspiracy) is beginning to realise the identity of the real enemy behind the conflict. Meanwhile, Sheryl decides to sing again with a brand new perspective.

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.