In the Mai-HiME manga, Nagi is a much more malevolent figure than in the anime. From his first appearance, it is clear that he is the one directing the Orphans against the HiME. Nagi appears out of nowhere as in the anime, often carrying a book, but his actions and words are openly malicious. He maintains secrecy about his own allegiance and purpose and violently attacks anyone who tries to disclose the truth. He is apparently killed by Miyu Grear in volume 3, when he had almost escaped an ambush organized by the combined HiME teams and Mashiro. However, this was proven to be false, as multiple copies of him appeared inside the Obsidian Palace, and continued to multiply themselves even during battle. They all fought Miyu, who continued to fight them even after most of her weapons had been used up, till the HiME star collapsed upon itself and became a unique Child.