Saori Kujo is a Valkyrie pilot in the all-female Faerie Squadron, commanded by Silvie Gena within the United Nations Spacy military. The squadron engages in combat against the invading Mardook forces threatening Earth.

Within Faerie Squadron, Saori operates as part of a trio alongside Amy and Nastasha. This group functions analogous to bridge crews, though their primary role involves piloting variable fighter Valkyries instead of capital ships. Saori develops a romantic interest in elite pilot Nexx Gilbert, occasionally acting to establish closer connections with him.

During the conflict's climax, Saori and her Faerie Squadron comrades join Nexx Gilbert in operating one of the Macross Cannon warships for Earth's final defense against the Mardook assault.