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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.

This OVA presents an alternate universe to the original Clannad anime, in which Okazaki Tomoya is dating Sakagami Tomoyo in the 24th and final episode of Clannad. When Tomoyo is elected Student Council President, her dream to save the school's cherry blossom trees from being cut down begins to come to fruition.

Included in the 8th and final DVD of Clannad ~After Story~ is an extra episode set in an alternate universe. Here, Fujibayashi Kyou is the main heroine in place of Furukawa Nagisa.