A young boy, Zero, is saved by a mysterious gunslinger who uses magical bullets. Later revealed to be Kurohime, she is the greatest magician in the world; however, she disappears shortly after saving him. Having fallen in love with her, he trains to become a gunslinger and ten years later, his search comes to an end, and both of them team up as fugitives running away from an angry warlord wanting to take his revenge on Kurohime for what she did to him 10 years ago. He finds that she has now been cursed by the gods, and now walks the Earth as a child by the name of Himeko. Her magic powers were greatly hindered as a consequence. The only way to revert the curse is for Kurohime to fall in love with somebody, a task that Kurohime is incapable of doing. However, experiencing crushes or infatuation causes the spell to be broken momentarily, allowing for the couple to get out of bad situations.
Later in the manga, Kurohime realizes at last that she is in love with Zero. With Kurohime now being able to love, the curse is finally broken, but the gods sent the God of Death together with the goddess of benevolence, Shirohime, to defeat and kill Kurohime because of her crime of having killed a minor god. At the God of Death's command, Shirohime seals Kurohime back into her child form again, called Himeko, using a spell that can never be broken, and the God of Death starts trying to kill Kurohime and Zero. During this battle, Kurohime's past is revealed through a flashback. It is revealed to be only half of herself as she was split into 2 when she challenged the gods years ago. This is due to the fact that the world was split apart with warring, as everyone was trying to prove themselves worthy of the promise of divinity given to the strongest human in the world. 10 years ago, Kurohime decided to end all the wars by pretending to be interested in becoming a god, but her real intent was to be able to ascend into heaven and start killing the gods instead.
Because Kurohime operates on a mentality of "ends justify the means," she was willing to sacrifice as many lives in order to end the war, such that the rest of the world and humanity might have absolute peace. Therefore, when the gods were deciding what to do with her, they decided to cut her into half and cleave her into "love" and "hate" which became Shirohime and Kurohime respectively. Shirohime then became a goddess, and in order to protect her other half, she sealed her with the curse that could only be broken with love, and sent her down to earth in her child form. During the climatic battle between the God of Death and Kurohime, Shirohime realizes that she has lost sight of the point of her existence, which only Kurohime can now fulfil, so she willing sacrifices herself to save Zero and Kurohime. With the death of her goddess counterpart, Kurohime regains her full power and defeats the God of Death. However, the latter had summoned the 'River of the Dead' in a last-ditch effort to defeat Kurohime. Anyone living being caught in the river will be dissolved. The only way across is to use the "Boatman of the River"'s boat, but it can only carry one person.
Zero sacrifices his life to push the boat, with the unconscious Kurohime inside, across the river. Witnessing Zero's death causes Kurohime to develop a trauma which seals her power, turning her back into Himeko, but this time with the appearance of a mid to early teen. However, she is capable of reverting back to her adult form and power, but every time she does, she loses some of her memories of Zero.
In a cruel twist, the gods later resurrect Zero as the new God of Death, to try and kill Kurohime. Having been stripped of his free will, Zero battles Kurohime, who cannot bring herself to fight the man she loves. As a consequence, Kurohime loses most of her memories of Zero. The released memories free Zero's mind, right before he completely becomes the new God of Death. However, Zero now possesses a significant amount of darkness in his heart. It is revealed that this is his "true self."
To understand his darkness and past, Kurohime travels 10 years into the past, before the war against the gods, and begins to witness what happened to Zero and his little brother.