Wir schreiben das Jahr 2199. Die Menschheit verliert den Krieg gegen die Gamilas und steht kurz vor der endgültigen Auslöschung. Inmitten eines Treffens der letzten Flotte der UN Cosmo Navy und der Gamilas beim Pluto stürzt ein mysteriöses Raumschiff auf dem Mars ab. Was hat die Nachricht zu bedeuten, die von diesem Schiff aus abgesendet wurde?
In the year 2199, Earth is ravaged by attacks from alien beings of the the planet, Gamilus, which have devastated the surface of the Earth and forced what remains of mankind to take shelter underground. To save the Earth, the last of the Earth's space forces must distract the Gamilan forces while a non-Gamilan ship, the Amaterasu, lands on Mars to deliver the Wave Motion Activation Core to the Earthlings. While Captain Mamoru Kodai contains the enemy attack to allow fellow captain Juzo Okita to escape with his forces, Mamoru's brother Susumu and his friend Daisuke Shima investigate the Amaterasu that crashed on Mars. Inside the ship there is the corpse of an alien female, the messenger sent to Earth to make the important delivery to the Earthlings. Susumu and Daisuke return to Earth on the Kirishima, the only ship to return from the battle at Pluto. On the Kirishima, Susumu learns of his brother's death. When the Kirishima reaches Earth, Susumu Kodai looks for Captain Okita to know whether his brother was a decoy or not and meets Yuki Mori, who directs him to the hospital wing. Kodai confronts Okita, who says that it was he who led Mamoru to his death.
Nell'anno 2199, la Terra è devastata dagli attacchi di esseri alieni del pianeta, Gamilus, che hanno devastato la superficie della Terra e costretto ciò che resta dell'umanità a rifugiarsi sottoterra. Per salvare la Terra, le ultime forze spaziali terrestri devono distrarre le forze Gamilan mentre una nave non Gamilan, l'Amaterasu, atterra su Marte per consegnare il Nucleo di attivazione del moto ondoso ai terrestri.
西暦2199年。ガミラスとの戦いに敗れ滅びゆく地球人類。国連宇宙軍最後の艦隊が冥王星沖にてガミラスと交戦する最中、火星に謎の宇宙船が不時着する。その宇宙船からもたらされたメッセージとは……!?
西元2191年，地球人類於史上首次與地球外智慧生命體接觸，兩者之間並引發戰端。對方名為「卡米拉斯」。由於卡米拉斯冥王星基地發射的遊星炸彈對地球進行轟炸，地球瀕臨毀滅，人類將要滅絶。
2198年，地球接收了來自異星人行星「伊斯坎達爾」的「次元波動引擎」技術供應，並得知對方擁有使行星取回原本面貌的「宇宙回復系統」，能拯救地球。於是便開啟了宇宙戰艦「大和」號的建造計劃。
2199年1月，人類距離滅絶只剩下一年的時間。在將自火星取得的「波動核心」被裝進「大和」號後，「大和」號帶著人類最後的一線希望，踏上了這場以一年為限的33萬6千光年的旅程，前往大麥哲倫銀河星球「伊斯坎達爾」
