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.

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!