Utawarerumono is a story centering around the masked protagonist, Hakuoro, who one day is found by a family of two girls and their grandmother in a nearby forest close to their village. He is badly injured and is soon found to have amnesia, so they take him to their home and treat him until he is well again. Hakuoro is soon accepted into their village where he stays and lives with them, but before long Hakuoro finds that life in this village is being oppressed by the greedy emperor who rules over the country their village resides in. Soon after, these negative actions taken towards their village result in him leading a rebellion against the emperor of the country which later lands him to become emperor of a vast new country which is named Tusukuru, after the well-respected woman who helped saved his life.

After becoming emperor and things begin to calm down, Hakuoro soon finds out that peace is hard to maintain and finds himself constantly in battle in order to protect the peace of his country and his people. Eventually, he is led into many bloody battles in order to fight for the freedom of all those residing in Tusukuru. Along the way, Hakuoro meets several other strong warriors from several other countries and tribes who are fully accepted into Hakuoro's growing family. Many moments of hardship and laughter ensue as time continues but with Hakuoro leading the way, all others are confident in his ability to lead.

The story's genre is at first a fantasy-style story with heavy Ainu influence, though later develops science fiction themes towards the end. Indeed, it first appears to take place in a fantasy world, fully with magical beings and interesting new species of humans, but it is later revealed that it takes place in a post-apocalyptic Earth's far future.