Plot
In 2015, a space expedition fleet led by Admiral Yuzo Takaya is destroyed by space monsters. Six years later, Takaya's daughter Noriko, a freshman student, enlists in the Okinawa Girls' Space Pilot High School (沖縄女子宇宙高等学校) in Okinawa.[4] She is selected with senior student Kazumi Amano to represent Japan in an upcoming space expedition. When the students know Noriko is the daughter of Yuzo and that Coach Koichiro Ohta was one of the survivors of the 2015 space attack, Noriko is subjected to bullying and harassment. Ohta, however, believes Noriko has the same potential as Kazumi, and through "hard work and guts" (努力と根性), she strives to become the best Machine Weapon pilot and take control of the experimental giant robot Gunbuster (ガンバスター) to help Earth win the war against the space monsters. Senior student Reiko Kashiwara challenges Noriko to a Machine Weapon duel, but Noriko defeats Kashiwara. Noriko, Kazumi, and Ohta fly off to the Silver Star orbital base.
Noriko, Kazumi, and Ohta meet Captain Tatsumi Tashiro and Soviet pilot Jung Freud. Kazumi and Jung duel with each other until the duo and Noriko find the remains of a space monster, triggering memories of Noriko's father's death. When the Silver Star detects an unidentified object speeding near Neptune's orbit, Ohta has Noriko and Kazumi investigate the object, later discovered to be Luxion, as part of their sub-light-speed training. Noriko unsuccessfully tries to search for her father. She, Ohta, and Kazumi return to the Silver Star, with six months having passed in the space battleship Exelion's non-relativistic frame, and its construction having just been finished.
On the Exelion, Noriko meets American pilot Smith Toren and develops feelings for him. Noriko pairs up with Smith on her first battle against space monsters after Kazumi dissolves their partnership out of fear for Noriko's safety. Smith is killed, and Noriko feels bad for being unable to help him. She begs Ohta to train her further to prove herself to Kazumi.
Jung challenges Noriko to a duel, but Noriko breaks down when space reminds her of Smith's death. On the Exelion fleet's way back to Earth, space monsters attack it. Tashiro orders the Exelion to perform a kamikaze run on the enemy flagship, but Noriko launches in the uncompleted Gunbuster to deal with the alien threat. Noriko single-handedly destroys the flagship, allowing the Exelion to return to Earth.
Ten years pass, Noriko and Kazumi graduate high school, and the Top Squadron disbands. Ohta sends Noriko and Kazumi to escort the decommissioned Exelion to the center of the space monsters' gathering and detonate its degeneracy reactor. Kazumi breaks down, as Ohta has been diagnosed with space radiation syndrome and has less than six months to live. Noriko and Kazumi combine their ships to form Gunbuster to protect the Exelion from oncoming attacks. They retreat before the Exelion explodes, creating a black hole that takes out the entire space monster army and parts of the Solar System. Gunbuster returns to Earth more than six months later, and Kazumi discovers that Ohta is still alive.
Sixteen years later, Kazumi pays her respects to Ohta after he dies. She goes to Hawaii to see an officer for Project Carneades. She warps to Sagittarius A* to rendezvous with the Eltreum fleet to deliver Buster Machine 3, which is the planet Jupiter compressed into a bomb powerful enough to destroy the space monsters' star system. The fleet and Gunbuster protect the bomb from waves of space monster fleets. The bomb is activated, but fails to detonate, as heavy damage during the battle reduced its energy output to 98%. Noriko and Kazumi go into the bomb and use Gunbuster's main degeneracy reactor to trigger its detonation. The Eltreum fleet warps back to Earth, leaving Gunbuster behind as it outruns the bomb's massive explosion. Gunbuster escapes the black hole and returns to the Solar System on July 6, 14,292. Noriko and Kazumi see that the Earth is dark, but a light pattern appears, saying: "WELCOME HOMƎ!" (オカエリナサイ). Noriko and Kazumi eject from Gunbuster and fall back onto Earth.