Un día, en el camino a su instituto, Tomoya Okazaki conoce a una extraña chica llamada Nagisa Furukawa. Más adelante en el día, Tomoya tiene una conversación con Nagisa durante el almuerzo y se entera de que ella está repitiendo su último año de escuela secundaria. Ella también dice que quiere unirse al Club de Dramatización, pero en ese año se había disuelto. Después del instituto, Tomoya va a la panadería de la Familia Furukawa y conoce a los padres de Nagisa. Ella invita a Tomoya a quedarse a cenar con ellos.

Nagisa admite que quiere recomenzar el Club de Dramatización y Tomoya la ayuda para crear carteles publicitarios, los cuales se colocan alrededor de todo el instituto. Ese día en el instituto, Tomoya conoce a otras dos chicas: una extraña chica superdotada llamada Kotomi Ichinose y una de primer año llamada Fuko Ibuki. Más tarde, en el mismo día, Nagisa descubre que Tomoya jugaba al baloncesto y lo invita a jugar un partido al día siguiente. Sin embargo, más tarde se revela que Tomoya resultó herido en el hombro en una pelea con su padre; como resultado, Tomoya ya no es capaz de jugar al baloncesto.

Después de los acontecimientos del día anterior, Tomoya va a visitar a Nagisa para ver si está bien y se entera de que ella es débil físicamente durante toda su vida. Mientras caminaba de vuelta a la panadería, Tomoya ayuda a conseguir salir de un aprieto a un extraño electricista y le da su tarjeta a Tomoya, enterándose de que su nombre es Yusuke Yoshino; más tarde, Youhei Sunohara, el mejor amigo de Tomoya, revela que Yusuke es un músico profesional retirado. Después de instituto del día siguiente, Tomoya ayuda a Nagisa a obtener más confianza a sí misma para el Club de Dramatización.

Dado a que no hay nuevos miembros en el Club de Dramatización, Tomoya va a hablar con Kotomi una vez más acerca de unirse al club. Tomoya la lleva por los alrededores del instituto y la ayuda a introducirse a sí misma con la gente y hacer amigos. Tomoya lleva a Kyou, Ryou y Kotomi al salón del Club de Dramatización después de clases y después de una ronda de presentaciones, Tomoya les pide unirse al club. Kyou no acepta en un principio, pero termina por ceder cuando su hermana y Kotomi dicen que quieren unirse. Durante la reunión, Kotomi se va cuando oye a alguien tocar el violín, aunque cuando se le da la oportunidad de tocar, ella lo hace realmente horrible, haciendo doler los oídos.

Con el fin de ayudar a Nagisa a reformar el Club de Dramatización, sus amigos ofrecen sus nombres con el fin de obtener suficientes nombres para calificar, pero todavía necesitaban un asesor para el club, lo que los lleva a preguntarle a Toshio Koumura. Sin embargo, éste ya estaba destinado a ser el asesor del Club de Coro, por lo que Nagisa va a hablar con Rie Nishina.

El Club de Dramatización es finalmente restablecida y Koumura es compartido con el Club de Coro. Al ver la tensa situación entre Tomoya y su padre, Nagisa ofrece tener a Tomoya en su casa, por el momento. Después de regresar del instituto, Tomoya encuentra a varios niños pequeños en la casa de Nagisa y se entera de que Sanae les está instruyendo en una escuela abandonada. Nagisa le dice a Tomoya que ella siente que hizo algo muy malo a sus padres en el pasado, pero no puede recordar lo que es y sus padres le dicen que ella debe estar imaginando.

Después de que Nagisa se entera sobre el pasado secreto de sus padres, ella no puede apartar de su mente el cómo arruinó los sueños de ellos y cae emocionalmente. En el día del Festival Escolar, todo el Club de Dramatización se da cuenta de que Nagisa no es la misma de siempre y tratan de animarla, pero los intentos fueron en vano. Cuando se inicia la actuación, Nagisa rompe a llorar, pero con las palabras de Akio, quien dijo que el sueño de Sanae y de él era que Nagisa haga sus sueños en realidad; finalmente la obra termina siendo un éxito. Al día siguiente, cuando el sol se pone, Tomoya finalmente confiesa su amor a Nagisa en el salón del Club de Dramatización. Esto viene como un pequeño shock para Nagisa, lo que la hace llorar de alegría.

Mei has become worried about her older brother since he still does not have a plan after high school, and comes to stay at Nagisa's for the time being. Based on a fleeting comment by Youhei, Tomoya gets the idea to ask a girl to pose as his girlfriend so Mei will stop worrying about him. Youhei goes around with Tomoya and Nagisa asking Ryou, Tomoyo, Kotomi, and Yukine, but no one can help him. Sanae overhears Youhei's trouble and decides to be his fake girlfriend if it will help push him in the right direction in life. Youhei, however, still believes her to be Nagisa's older sister. When Mei meets her brother's "girlfriend", Sanae is posing as a student from Tomoya's high school.

Tomoya and Nagisa visit Youhei, and spend some time talking with Misae and Tomoyo who comes over after them. Later, when Tomoya and Nagisa are talking with Misae privately, Tomoya starts falling asleep. It is shown how when Misae was a first-year in high school, she met a strange boy named Katsuki Shima who says he can grant her one wish in return for her cheering him up years before when he was in the hospital. Misae has a boy she likes named Igarashi, but who unknown to her already has a girlfriend. Igarashi asks Katsuki to tell her this, but he cannot tell her directly and starts crying. Misae sees Igarashi with his girlfriend, and realizes the truth; she runs away, leaving Katsuki behind.

Tomoya, Nagisa, and Youhei finally find out that Yukine is respected by the two rival gangs in the city since she helps both sides' members after they get hurt. Her older brother is the leader of one of the gangs, and a young boy named Yu comes to her to find his older sister who apparently is dating a guy in Yukine's brother's gang. Youhei tells Yu that he is Yukine's brother for a time, but the truth is later revealed after Yukine takes Yu, along with Tomoya, Nagisa, and Youhei, to a bar where her brother's gang hangs out. Yukine's brother has been in the hospital since he saved a friend and got in a car accident. While heading home, three members of the rival gang think Youhei is Yukine's brother and try to fight him and Tomoya, but Tomoyo intervenes, stopping them single-handedly.

Tomoya and his friends are nearing graduation, and are discussing what they will be doing after they graduate. Kyou wishes to be a kindergarten teacher, Ryou hopes to go to a nursing school, Kotomi wants to study in America, and Youhei aspires to be a model. Tomoya still has not decided on what to do yet. Nagisa's sickness returns, making her unable to go to school and take exams. On the day of graduation, Tomoya returns home to Nagisa who wishes to take a walk with him, while holding hands.

Shortly after his graduation, Tomoya decides to be more independent, and works toward this goal by first taking up a job at the bakery. Meanwhile, Nagisa has begun her new school year, although she makes few friends and her attempt to reestablish the theater club ends in failure. Tomoya eventually moves out of Nagisa's home to a small apartment of his own, while taking up a job as an electrician with Yusuke Yoshino. After his first day of work, Tomoya returns to his home completely exhausted, barely able to stay awake during his dinner with Nagisa.

Winter comes and Nagisa enters the final months of her pregnancy, but she becomes sick again. On a snowy day, Nagisa goes into labor two weeks early and her family, unable to transport her to a hospital in time, is forced to have her give birth at home. After an excruciating process, Nagisa successfully gives birth to her daughter, Ushio, but the delivery and her illness combined take their toll on her and Nagisa dies moments after seeing her newborn baby. Tomoya, who has stayed by her side for the entire time, does not take the sudden turn of events well. His dream of raising their daughter together as a family is shattered.

Five years after Tomoya left Ushio with Sanae and Akio, he spends his days at work and spending money on smoking and drinking. Sanae and Tomoya go out together into town, and she asks him to go with her and Akio on a family trip; after Sanae continues to ask him, he accepts. The day of the trip, he discovers that both Sanae and Akio have left him and Ushio alone together. The two spend the next day and night together, and when Sanae and Akio still do not show up, Tomoya asks Ushio if she would be willing to still go on a trip, even if it was only with a person like him. The two decide to take the trip by themselves and, as they walk, Tomoya wonders where they are headed.

Ushio's fever does not back down and Tomoya decides to stay home to take care of her. In case he had to leave home, he calls for both Akio and Sanae to take his place. Ushio tells Tomoya that she wants to go on a trip again like last time, but he declines and tells her that it will happen once she gets better. After resigning from his work, Akio offers him some money, but Tomoya declines his kindness and Akio states that every man has something to protect. After several months, winter arrives, and Ushio's fever still does not back down, and Tomoya seems to be getting sick too. Ushio once again ask Tomoya to go on a trip, and he ultimately accepts thinking that he might not be able to fulfill another promised wish. After they leave the house, Ushio's fever worsens, and she dies in his arms right after telling her father that she loves him. Soon after, Tomoya collapses as well.

The girl in the Illusionary World is dying in the snow, and the robot regrets having her take the journey. The girl can finally hear the robot, and tells him that they once existed in another world. As she hums the tune of "Dango Daikazoku", the Illusionary World starts to collapse. As the robot is swept away, the girl calls him "Papa" and disappears with the world. Back at the hill, Tomoya calls after Nagisa, and she is glad that he did so. Nagisa brings Tomoya through time, and together the voices of the robot and Tomoya note the end of his long journey. Tomoya awakens to Ushio's birth, but this time, Nagisa miraculously survives. After Nagisa watches Tomoya give Ushio her first bath, she and Tomoya see that countless orbs of light are floating throughout the city outside the window. They both sing to Ushio and from then on, Tomoya and Nagisa experience a happy life raising their daughter together, finally free of their cursed fate.