Innocent Lilies: The End And The Beginning by Koichi Sakamoto

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Shiro Majo Gakuen ("White Witch Academy") is a secret garden that accepts girls who have been emotionally injured. Moga becomes a white witch after receiving training and leaves Shiro Majo Gakuen to save the world, but a white witch, Rina, appears in front of her. Also, black witches, who are hostile to the white witches and are attempting to create a new world with a spell, appear in front of her. Later, Moga sneaks into Kuro Majo Gakuen ("Black Witch Academy") to save Rina after she was kidnapped. There, Moga sees a girl who once stayed with her at Shiro Majo Gakuen.