Nagisa is the main heroine of Clannad. Although she is in her third year in high school, as is Tomoya, Nagisa is actually one year older since she had to repeat her third year after an illness that lasted nine months. On the first day of school, She meets Tomoya on a long hill path in front of the school. She has a strange habit of muttering the names of food that she plans to eat as a way to motivate herself, such as anpan. She wants to reestablish the once-disbanded drama club. She does not have much self-confidence so she often needs help in order to motivate herself through the day.
The major arc of the story revolves around Nagisa. After Tomoya befriends Nagisa, she tells him of her dream of joining the drama club. They soon discover that the club was disbanded, and has no members anymore. While attempting to recreate the club, Nagisa and Tomoya discover that they cannot advertise for new members, having missed the deadline to do so. In order to create an officially recognized club, they find they need at least three members and a sponsor teacher for the club, and the only one left is Koumura, who asks them to discuss with the chorus club members. After listening to Rie's story, Nagisa gives up reestablishing drama club. Youhei is furious about the story, and decides to have a 3-on-3 basketball match with the basketball team to prove that the chorus club members cannot hide behind their handicap. This happens to be a success, since the chorus club members decide to share Koumura with the drama club.
After Tomoya had a falling out with his father, Nagisa offers to have Tomoya move into her house until things settle down, to which Tomoya agrees. Curious about Nagisa's play which is the same as the illusionary world he dreamt, Tomoya tries to find about the story, which leads him to learn about the secrets behind Nagisa's sickness. Nagisa later also learns of the secret and becomes guilty about unknowingly forcing her parents to give up their dreams. However, this changes once her parents tell her that since that day, they had changed their dream to hers, and with the help of Tomoya, Nagisa regains the mental strength to act out her drama. Nagisa later succumbs to her sickness again, and is forced to repeat her third year again in After Story.
After Story is a continuation of Nagisa's story, where Tomoya works as an electrician, and Nagisa starts living together with Tomoya. In this story, Nagisa faces a tragedy and continues to battle with her sickness. She also successfully gives birth to Ushio, the daughter of her and Tomoya, however Nagisa dies shortly afterwards. If Tomoya manages to collect the needed amount of light orbs, a miracle will happen using all the light orbs, and Nagisa safely delivers Ushio without dying, thus ending Tomoya's "journey with the light". Nagisa, Tomoya and Ushio are able to live together as a family without facing their doomed fate.