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.

Alto and Ranka make an emergency landing in planet Galia 4 due to a malfunction with their variable fighter.

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.

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.