Noriko and Kazumi arrive at the space fleet led by the space battleship Exelion. The girls get introduced to a hot shot female fighter named Jung Freud. During one of their mech training sessions, Jung spars with Kazumi, and end up in a part of the station where they discover one of the mechs of their enemy. Later on, Noriko and Kazumi are sent to partake in a special mission to investigate an object traveling at near light speed. With the laws of quantum physics and time dilation, the mission that would normally take just a few minutes will span several months. But they discover the object is the Lexion, the ship that Noriko's dad used to command.

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.

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."