The Exelion prepares to jump through hyperspace. All the girls and guys are confined to their quarters during the mission, but Noriko loses a dare game, and has to wander off in the dark. She is surprised when a person shows up, but it turns out to be a charming guy named Toren Smith, who befriends Noriko. They get into some minor trouble for being out, and as punishment, they have to polish the lenses for the laser cannon array. But then the Exelion gets a surprise fly-by by the enemy. The fleet goes after them for a large battle at Leaf 64. Toren offers to be Noriko's partner for the next battle, since she has fallen out of favor from Kazumi. But trouble arises as they get overwhelmed by the sweeping enemy.

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."