Picking up where Clannad the series left off, Tomoya has confessed his love for Nagisa, taking their relationship to a new level and direction. The second semester starts and Tomoya continues to meet new people, who alter his perspective of family and relationships. As time passes, the path which Tomoya and Nagisa walk is filled with challenges and struggles that will test the strength of their love.
With summer drawing to a close as the new semester begins, Nagisa’s father, Akio, is putting together a neighborhood baseball team. Tomoya recruits several other students to join the team. During a game against the team from a nearby shopping district, Akio is injured, threatening the small lead the team had built early in the game. Nagisa fills in, and in the end it all comes down to Tomoya.
Nagisa is worried about Mei's lack of focus. Mei comes to stay with Nagisa, and Tomoya thinks it's a good idea introduce Youhei to the ladies.
Youhei and Sanae double date with Tomoya and Nagisa but are also accompanied by Mei. Even though Sanae has convinced Mei that she is Youhei’s girlfriend, Mei is still worried and decides to stay. To get more of Youhei’s brotherly attention, Mei lies about her reason for coming to the city, saying that it was actually to meet a boy that she likes. Tomoya ends up getting pulled into playing that part.
Youhei's truant behavior worries his sister and his friends. In an effort to help him, they convince the soccer club to let Youhei back on the team. Although he has been readmitted to the club, he is not allowed to play on the team. The situation escalates when the team leader bullies Mei and makes her cry, resulting in a fight between the team, Youhei, and Tomoya.
Misae recalls a time when she comforted a boy named Katsuki Shima in the hospital. Years later, they reunite, and Katsuki wants to repay her kindness. Misae's feelings for Igarashi will soon become more complicated than she thought, as he has a girlfriend.
Misae starts to get over Igarashi and begins to spend more time with Katsuki. She realizes she has feelings for him, but Katsuki's own revelation prevents them from being together.
When Yukine came to the aid of two rival gangs in the city, she has since earned their respect. The fact that her older brother, Kazuto, is also the leader of one of these gangs helps. A young boy approaches Yukine out of concern for his older sister, who is dating a member of Yukine’s brother’s gang. Yukine’s brother has been in the hospital following a car accident and three rival gang members mistakenly believe that Youhei is him.
The police have become more determined to curtail gang violence in the city. Tomoya and Yukine go to talk with the rival gang, to try to keep matters from escalating. The leader suggests a one-on-one fight between himself and Kazuto to settle all scores.
The school year is coming to a close and everyone is discussing what they plan to do after graduation. Everyone has their own plan of what they want to be, except for Tomoya. Nagisa becomes ill again and misses her exams. On graduation day, Tomoya takes Nagisa for a long walk.
Tomoya takes a job at a bakery, hoping to become more independent. Nagisa returns to school and tries to revive the theater club. Tomoya then takes an electrician job with Yusuke and moves into his own apartment.
Tomoya is eager to show his boss and coworkers that he is a valuable worker, even hiding the fact that he has injured his shoulder. Though he promises to go with Nagisa to the Founder’s Festival, he stays at work, showing up late for his date. His boss and coworkers hold Tomoya in high regard, but the work is taking a toll on his relationship with Nagisa.
Yusuke tells Tomoya about his past struggles and losses. After high school, Yusuke was a successful musician but got involved in drugs, which eventually ruining his career. Tomoya is offered a job as a manager, but his father is arrested, causing the offer to fall away. Finally, Tomoya proposes to Nagisa.
Tomoya is striking out trying to get Akio to consent to his marrying Nagisa. Akio says that he will speak on the matter only after Tomoya gets a decent hit in a ball game. After Tomoya finally hits a home run, Aiko gives his permission. Tomoya calls Nagisa’s friends together to celebrate her graduation. After receiving her diploma, Nagisa and Tomoya are married.
Nagisa and Tomoya are beginning their new lives together. Nagisa gets a job with Nishina in a restaurant. Tomoya gets upset when he learns that the school building that used to house the drama club will be torn down. Change upon change is happening all around them, but the biggest change to their lives is about to come.
Morning sickness is keeping Nagisa in bed. Sanae introduces her to a midwife, Yagi. Sanae confides to Tomoya her worries that having a child will be very difficult for Nagisa, perhaps even dangerous. Nagisa wants to have the child, despite the possible threats to her health and life. Akio recalls to Tomoya about the day Nagisa almost died and that, no matter what, he and Sanae will be there for them.
In the latter part of her pregnancy, Nagisa has become sick again and goes into premature labor. Due to the snow, she is unable to be taken to the hospital. She gives birth at home to a daughter, Ushio.
Tomoya has struggled with his grief and Ushio is being raised by Sanae and Akio. One day, Sanae visits Tomoya and persuades him to go on a family trip with them. When the day of the trip arrives, Sanae and Akio go out and do not return, forcing Tomoya to spend time alone with his daughter.
Tomoya buys Ushio a toy robot to play with. On their trip, the two walk through a flowery field and Ushio loses her toy in the grass. The two search the area and are joined by Tomoya’s paternal grandmother. She helps Tomoya remember that his father would take him to that field after his mother died. Ushio is very upset when they cannot find the toy, since it was the first present her father ever gave her. Tomoya realizes that he has acted just like his own father and resolves to not follow the same path.
After returning from their trip and visiting with Sanae and Akio, Tomoya brings Ushio home to live with him. On a day off, Tomoya and Ushio meet up with Kouko. Later, Tomoya takes Ushio to visit his father. The two reconcile and Tomoya urges him to move to the countryside and see his mother.
Tomoya goes to Ushio’s school to meet her teacher and finds that it is Kyou. Kyou tells him that the school will be having a sports day and encourages him to participate. Tomoya sings Nagisa’s song as a lullaby to his daughter. One day, when preparing to visit Nagisa’s parents, Ushio suddenly develops a fever.
Ushio does not appear to be getting any better and Tomoya remains home with her. Ushio tells her father that she wants to go on a trip again, just like the first one they ever took. Tomoya promises they will when she gets better. Months pass, and Ushio is still not better. Tomoya finally decides that they had better take their trip.
Sitting on the hill, Tomoya calls out to Nagisa, who appears and brings him back through time to see what their life could have been.
Tomoya looks back on his past.
Tomoya explores the life he could have had.
Tomoya tells his daughter the story of his life with Nagisa and how Ushio was born, but with a happier ending.