Garo: The Makai Flower follows Raiga Saezima, the son of Kouga Saezima and Kaoru Mitsuki, who after his parents' disappearance trained to succeed his father as the new Golden Knight Garo, being ultimately granted this honor after Kouga, who unbeknownst to Raiga is still alive somewhere, relinquishes his title to his son to act in his stead. After several years, he is tasked by the Senate to deal with Eyrith, a Horror whose power to revive the evil Messiah led Makai Priests of the past to seal her essence into a stone slab by means of splitting her into nine lesser Horrors. In the present day, this seal has been undone and these Horrors roam freely, even though one possesses Eyrith's seed which will bloom if it cannot be sealed once more. Raiga is assigned to stop Eyrith, and to that end the Senate sends Mayuri, an artificial being resembling a young human woman, who has the power to seal the Horrors of the slab back into stone after the Horror is slain by a Makai Knight. They must act before one of the nine Horrors awakens Eyrith's seed. To further assist them, the Senate also assigns the Shadow Knight Crow to assist Raiga and Mayuri in their mission to prevent Eyrith from blooming and bringing Messiah back into the realm of the living.