A estória de Macross F se dá no ano de 2059 (três décadas após as maiores seqüências, Macross Plus e Macross 7), a bordo da 25ª Macross Frontier, esquadra de colonização de super-longa-distância, com 10 milhões de habitantes. Ranka Lee (interpretada pela estreante Megumi Nakajima) dirige-se ao show do maior ídolo da Rede Intergalática de Macross Frontier, Sheryl Nome, quando encontra um piloto aprendiz chamado Alto Saotome - e quando um inimigo misterioso ataca a esquadra. A estória também apresentará o irmão mais velho de Ranka, o piloto veterano Ozma Lee, e o mais novo mecha das Forças da ONU, o VF-25.
Kenta Miyake • Katsuyuki Konishi • Sanae Kobayashi • Tomomichi Nishimura • Hiroshi Kamiya • 田中理恵 • 中島愛 • 桑島法子
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.
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.
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.
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.
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.
