After being threatened by extinction at the hands of alien invaders called the Zentradi, humanity undertook the task of guaranteeing itself a future by launching fleets of colony ships into space. On Macross Frontier, one such fleet, high school student Saotome Alto's life is changed forever: the fleet is suddenly attacked by unidentified creatures while he is performing aerial stunts for a concert by the wildly popular idol Sheryl. Alto quickly finds himself in the cockpit of a new-model fighter, struggling to protect Ranka Lee, a young girl he met only hours earlier, from the invaders' swath of destruction. Noting his performance during this incident, the S.M.S. Skull Squadron private military company invites Alto to join their organization, where he continues protecting his friends and Macross Frontier.
The members of S.M.S Macross Quarter investigate the truth behind the destruction of the 117th Large Scale Research fleet in a Vajra attack and Ozma Lee finds the shadow of Grace O' Connor's ambition present in the incident where Ranka lost her family. Meanwhile, the NUNS military forces of Frontier prepare for a final decisive battle to protect the fleet from the Vajra.
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.
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.
Mr. Bilrer, the owner of S.M.S. meets with Alto Saotome. At the same time, Ranka finds out that Brera, the pilot of the hostile VF-27, has been listening to her songs.
Ranka prepares a special gift for Alto's approaching birthday.
Due to repeated Vajra attacks, the Frontier colonial fleet's resources are shortened. Energy becomes limited, and water and food rationing increases the population's unease.
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.
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.
Due to insufficient resources in the Frontier Fleet, food is being rationed. As even oxygen is being lowered inside the colony, Alto cooks for a V-virus infected Sheryl as they pass the time peacefully. Right after that, Alto receives a shocking revelation about the origin of the Vajra and the power behind Ranka's song from Mr. Bilrer and Leon Mishima. Meanwhile, Brera and Ranka arrive at the the Vajra home system. However, they were soon attacked by Vajra patrols and Ranka was captured. While fighting his way towards Ranka, Brera encounters Grace O'Connor, who took total control over him using an obedience override in his cybernetic implants.
Ranka Lee is contracted to act in a minor role during a movie about the legend of Shin Kudo, while Sheryl Nome is the main female protagonist of the film.
Ozma promises Ranka to attend her first live concert on Macross Frontier, but he is ordered to defend the fleet from another Vajra attack before that.
The secret of "Aimo", the lullaby that only Ranka and Brera know is finally revealed.
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.
Sheryl gives a consolation concert at planet Galia 4, but because of an undisclosed illness she cancels her concert, which causes a huge riot.
Alto and Ranka make an emergency landing in planet Galia 4 due to a malfunction with their variable fighter.
Sheryl's manager Grace O'Connor informs Mikhail Buran about his elder sister. Mikhail gets troubled by it and during a battle with the Vajra he almost hits Alto Saotome by mistake, which causes trouble between the two.
Ranka Lee is scouted by an entertainment production company. While Sheryl is rehearsing for her Sayonara live concert on the final day of her tour, news arrives that the Macross Galaxy fleet is being attacked by a large horde of Vajra. As a result, President Howard Glass decides to inform his citizens of the new enemies' existence.
Ranka transfers to Mihoshi Academy so as to be able to pursue a career in entertainment. A visit by Sheryl to Ranka's new school causes chaos in the academy.
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.
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 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.
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.
Sheryl comes across Alto again in her quest to find her missing earing. She orders Alto to guide her around the Macross Frontier fleet. Elsewhere, Ozma and Ranka argue about her decision of becoming a singer.
Alto Saotome unexpectedly meets Ranka Lee and Sheryl Nome again at an observation park. However, the Vajra also shows up in the skies above the three, so they immediately head to the park's emergency shelter and get trapped inside.