Noriko Takaya has spent barely had a month at a training school for giant robots. The school announces they are going to select two candidates to go to the Exelion spaceship for the real missions to fight against an invading mech army. One of the choices is obviously the beautiful and leading senior Kazumi Amano, but somehow Noriko is selected for the second spot! The other girls get jealous that Noriko got the spot, suspecting it's because she was the daughter of the Admiral in a previous mission. School rival Reiko Kashihara feels that's totally wrong, and challenges Noriko to a duel.

Fifteen years later, Kazumi is called to another mission, to detonate a black hole bomb in the enemy's home galaxy. She joins Noriko and Jung as they pilot the Gunbusters to their final destiny that could mean the "extinction or survival of the human race."