Something bizarre has come over the land. The kingdom is deteriorating. People are beginning to act strange... What's even more strange is that people are beginning to see dragons, which shouldn't enter the world of humans. Due to all these bizarre events, Ged, a wandering wizard, is investigating the cause. During his journey, he meets Prince Arren, a young distraught teenage boy. While Arren may look like a shy young teen, he has a severe dark side, which grants him strength, hatred, ruthlessness and has no mercy, especially when it comes to protecting Teru. For the witch Kumo this is a perfect opportunity. She can use the boy's "fears" against the very one who would help him, Ged.

A film adaptation of the Holy Emperor story arc, which primarily depicted the conflict between Kenshiro and Souther. New characters Reina, one of Raoh's army officers who falls in love with him, and her brother Soga, Raoh's advisor, play an important part with much of the plot involving Raoh's relationship with Reina as he conquers the land; most of this portion is new content exclusive to this film. The other side of the story is the retelling of Ken's attempt to save and protect the villagers from Souther's army with the help of Shū. There is also a small subplot of Bart returning to his home.

愚蠢的人类被贪婪所驱使，按下了那枚摧毁文明的按钮。浩劫过后，人类世界退回到暴力血腥的原始阶段，而在这混乱的世道中，拉奥所统领的拳王军所向披靡。当初，拉奥作为大师兄，曾和健四郎一同学习北斗神拳。这个有着1800年历史的暗杀拳法，始终奉行着唯一继承人的准则。拉奥虽然实力雄厚，却始终缺乏健四郎的悲悯之心。当后者成为北斗神拳的继承人化身为救世主时，拉奥转而走上更为黑暗的道路。当拳王军的铁蹄已经统治这个国家之时，南斗自由军揭竿而起，并邀请健四郎一同对抗他的宿敌——拳王拉奥…… 本片根据原哲夫、武论尊的经典漫画原著《北斗神拳（北斗の拳）》，是《真救世主传说 北斗神拳》的第三部。