Tomoya Okazaki is a Junior in high school and has had a very rough life. When he was little, his mother died in a car accident which made his Father turn to drinking and gambling. Due to his Father's behavior, Tomoya and his Father do not get along and Tomoya has become a delinquent. One day Tomoya meets a girl named Nagisa, and they start to hang out together. Tomoya is now beginning to think his life is about to change because of his new friend.
Tomoya Okazaski makes a new friend on the way to school named Nagisa Furukawa. She was held back for one year in school because of absenteeism. They become fast friends, so he decides to go to her parents' store to meet them.
On the way to school, Tomoya is almost hit by a girl on a scooter. It won't be his last strange encounter with a girl for the day.
Tomoya is on his way to Nagisa's house for a visit but ends up going to Youhei's house instead. The next day he helps Nagisa out with her theater club.
The Student Council has decided that Nagisa cannot reestablish the theater club. As Tomoya and Youhei are helping Nagisa recruit students to the club, they come across the ghost of a girl who was killed in a car accident.
Tomoya and Nagisa decide to investigate whether Fuuko is really Ibuki's sister. After meeting her, they congratulate her on her engagement. This confuses Ibuki, as she only told Fuuko about her engagement. Nagisa and Tomoya begin to wonder if Fuuko is the rumored ghost girl.
Fuuko tries to find people to attend her sisters wedding. Nagisa invites Fuuko's sister to the Founders Festival.
Tomoya receives some shocking news about Fuuko.
Fuuko is starting to fade from everyone's memory. This complicates things, as Kouko's wedding is coming up, and no one remembers the meaning of the starfish.
Tomoya, Nagisa and Fuuko spend the night at school. When they wake up the next morning, they cannot remember why they spent the night there.
Tomoya introduces Kotomi to Nagisa in hopes it will convince her to join the theater club. As Tomoya watches Kotomi and Nagisa speaking, he decides Kotomi needs more friends and sets out to help her form friendships.
Tomoya falls asleep at school only to awake to the sound of Kotomi playing the violin. A girl from the music room lent Kotomi the violin and now she wants everyone to hear her.
Kyou tries to purchase a stuffed elephant for Kotomi's upcoming birthday. Just as Kyou is about to give up, Fuuko appears and convinces her to give Kotomi a star instead. The next week Kotomi becomes very upset to learn of a bus accident.
Seeing Kotomi standing on newspaper clippings sparks Tomoya's childhood memories. Kotomi and Tomoya recall their childhood friendship, and Kotomi explores her feelings of regret.
Tomoya falls asleep in the garden after working tirelessly through the night. A mysterious stranger waits for Kotomi at school with the intention to steal her parents' thesis.
After she speaks with Toshio Koumura about becoming an adviser for their club, Nagisa recevies a letter to stop the theater club.
When Nagisa, Tomoya, and Mei visit Sunohara, they find her dorm in shambles and no sign of Sunohara!
After a basketball game, the choir club approaches Nagisa about the prospect of sharing Moumura as a mutual adviser between both clubs. After presenting this idea to the Student Council, Nagisa receives more bad news.
Tomoya has been suspended from school, so he hangs out in his room all day thinking about Nagisa. In an attempt to make him feel better, Kyou and Ryou take him to the arcade.
The theater club is finally established once Tomoya is named president of the student council. When a meeting between his father and his teacher approaches, Tomoya only wants to run away. Nagisa helps him face his issues with his father.
Nagisa wants to put on a play about a girl and a robot. While looking through a storage shed for reference books about the play, Nagisa and Tomoya are confronted by Akio.
Akio has a video to show Nagisa and Tomoya. The next day's rehearsal includes an energetic Nagisa who wants to put on a successful show.
The day of the festival has arrived, and Nagisa is so upset about what happened to her dad that she breaks down before she can perform in her play.
Tomoya's and Nagisa's relationship has become stagnant. Mei tries to help them by convincing Nagisa to open up her heart more to Tomoya.
An alternate ending reveals that Tomoya and Nagisa have been together longer than anyone thought. However, rumors have surfaced about the couple which make Tomoya feel like a burden.