Timid but hard-working high schooler Tetsu Misato takes up a job at his father's housekeeping agency, where he finds himself working at the mansion on the hill he always saw as a child. Deep in the back of the mansion lies a garden and a lone building, where the mysterious daughter of the house, Shizu Karasawa, lives in isolation.

While cleaning near the building, Tetsu chances upon the enigmatic girl, and when he returns the next day, they quickly get to know each other. Shizu reveals to him that she is confined to the building due to an unknown illness afflicting her, and that she has had no human interaction for years.

As they continue to meet, Tetsu's feelings toward Shizu develop—but when he realizes how he truly feels, he is faced with the true nature of her illness. Ohayou, Ibarahime follows Tetsu as he searches for the real Shizu underneath her supernatural condition—both for her sake and for the sake of his own feelings.