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Kodomo no Jikan is centered around 23-year-old Daisuke Aoki, who has just landed his first teaching job as a grade school instructor at Futatsubashi Elementary School (双ツ橋 小学校, Futatsubashi Shōgakkō). He is placed in charge of Class 3-1, where one of his students, a mischievously precocious nine-year-old girl by the name of Rin Kokonoe, develops a crush on him and proclaims herself as Aoki's girlfriend. At first he dismisses it as harmless, but she aggressively pursues her efforts to be with him. Aoki is in shock when she makes sexual advances towards him, thus leading him to believe that Rin comes from a troubled family. Aoki finds out that Rin's mother had died and she is living with a cousin whose flashbacks lead to violent outbursts.