Two years after the events of the Fourth Great Ninja War, the moon that Hagoromo Otsutsuki created long ago to seal away the Gedo Statue begins to descend towards the world, threatening to become a meteor that would destroy everything on impact. Amidst this crisis, a direct descendant of Kaguya Otsutsuki named Toneri Otsutsuki attempts to kidnap Hinata Hyuga but ends up abducting her younger sister Hanabi. Naruto and his allies now mount a rescue mission before finding themselves embroiled in a final battle to decide the fate of everything.

数千年后的未来，进入宇宙空间的人类，被分为银河帝国与自由行星同盟这两个拥有“专制政治”与“民主主义”两种不同政治体制的国家。两国之间的抗争持续了150年，以无边无际的广袤银河为舞台，重复着无止境的战斗。银河帝国的门阀贵族社会的腐败，以及在自由行星同盟中被称为“民主主义的弊端”的群愚政治正侵蚀着两个国家。之后，宇宙历8世纪末，两位天才的登场驱动了历史。“常胜的天才”莱因哈特·冯·罗严克拉姆，以及人称“不败的魔术师”的杨威利。两人率领着帝国军与同盟军，展开了不知道是第几次的冲突。