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Events in After Story take place immediately after the end of the first part, but extends into the next ten years, where Tomoya and Nagisa live together as a family. Life continues on for Tomoya.

Tomoya is labelled as a delinquent at his school because he is constantly late and skips classes, but he seems to have little care about how others perceive of him. Everything in his life seemed dull and unchanging until one morning he meets Nagisa Furukawa on the road to his school; he finds her muttering to herself to give her more motivation for the school day.