Kazumi and Noriko return to Earth for their high school graduation. Even though they are still teenagers after all these months in space, the Earth has aged ten years. Noriko meets up with her friend Kimiko, who now has a daughter. The Earth's forces discover that a massive number of alien spaceships are converging into the solar system. Coach has a strategy that involves creating a miniature black hole around Jupiter 2, but he will need Kazumi and Noriko to work together to pilot Gunbuster in order to put his plan into operation. However, Kazumi is having second thoughts as she's fallen in love with Coach and knows of his health situation.

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!