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Clannad is set in a high-school located in a town in Japan, which one isn't really specified. Okazaki Tomoya is a third-year student who doesn't take his studies seriously.

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.

Rintaro Okabe is a self-proclaimed "mad scientist" who believes that an international scientific organization named SERN is conspiring to reshape the world according to its own interests. He and his friend Itaru Hashida inadvertently create a gadget able to send messages to the past.

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.

Third-year high school student Koyomi Araragi barely survives a vampire attack, thanks to the help of Meme Oshino, a strange man who lives in an abandoned building. Despite being able to save his humanity, several powers from vampirism remained in his body as side effects.

The story revolves around Rin Okumura, a teenager possessing abnormal strength and endurance who, along with his younger twin brother Yukio, was raised by Father Shiro Fujimoto. Soon after Yukio departs to study at the prestigious True Cross Academy, Rin learns that he is the son of Satan, the strongest of all demons.

The distant future: Humanity established the mobile fort city, Plantation, upon the ruined wasteland. Within the city were pilot quarters, Mistilteinn, otherwise known as the “Birdcage.

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.

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.