The fleet advisor tells Captain that the aliens are going to attack Earth. Coach has been training Noriko, but Jung wants to test Noriko by challenging her to a duel. Noriko is still shaken from the death of her comrade and breaks down when they are outside. As the fleet is preparing to jump back to Earth, hoping to hide their trail in subspace, they are suddenly attacked by the aliens and everyone scrambles for their mechs. Noriko is benched for the battle. Things look bleak as most of the defense forces are wiped out, but Noriko manages to get out of her rut and moves to pilot the force's super prototype mech called Gunbuster.

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."

Nono, a young girl from the country, moves to the big city in order to achieve her dream: becoming a space pilot!

Nono's despair grows as her certainty that she'll get a Buster Machine fades.

With the survival of humanity itself at stake, one desperate plan remains: the sacrifice of the Earth, to strike at the beast! But where is Buster Machine #7?