In order to help Nagisa reform the drama club, her friends offer their names in order to get enough members to qualify, but they still need a teacher to advice them with the club, which leads them to ask Toshio Koumura. However, he is already meant to be the adviser for the choir club, so Nagisa goes to talk with Rie Nishina about which club Koumura should advise. The next day, Nagisa finds a threatening letter in her desk, and Youhei finds out that it was Rie's friend Sugisaka who is behind it. After talking with Nagisa about Rie's past, Nagisa chooses to give up on reforming the drama club, though this does not sit well with Youhei. Tomoya and Youhei go to Yukine Miyazawa to kill time during school, and Yukine gives Youhei an idea related to basketball. The next day, Youhei approaches Tomoya and Nagisa about playing in a basketball match in order to get the choir club to back down, but Tomoya continuously refuses his offer.

When Mei shows up, she cleans her brother's filthy room, but cannot stay at her Youhei's all-boy dorm, so Nagisa offers to have her stay at her home while she is in town. Tomoya and Youhei easily get Kyou to help with the basketball game, and she gets pumped up after a comment about pairing up with such loser guys. For half the game, Tomoya and the others play against first-year rookies, and manage to lead by eleven points, but then the basketball team switches with their starters and the score evens out. In the very last seconds of the game, Tomoya manages to make the last shot and win the game. Afterwards, Mei goes back to her hometown.

It is now during summer vacation, but despite now having been going out for weeks, both Tomoya and Nagisa are still very nervous about it and have not done much to progress their relationship which comes as a shock to their friends. Mei comes back for another visit and after learning of Tomoya's and Nagisa's current stagnant relationship, decides to be their personal cupid of love in order to advance things along. Mei thinks up a whole plan which Nagisa attempts to follow despite it being very embarrassing for her at times. After Tomoya calls Mei out, she runs away, though Nagisa stops Tomoya from chasing after her. With some time left in the day, Tomoya and Nagisa take a walk together.

Summer vacation is now over and the second semester has started at Tomoya's school. Nagisa's father Akio asks Tomoya to form a baseball team for a local game against the neighboring shopping district team. Tomoya is able to recruit Kyou and Kotomi from the drama club, Youhei and his younger sister Mei, Tomoyo, Misae, and Yusuke. Tomoya's team manages to get an early lead, but Akio's leg gets injured by a flying bat, and Nagisa fills in for her father as the pitcher. The other team catches up near the end, and it comes down to the final inning when Tomoya scores an RBI, winning the game.

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.

Yohei and Sanae go out on a date, accompanied by Mei, Tomoya and Nagisa. During the date the group witnesses a young girl being bullied by some slightly older boys. The scene is resolved by the girls older brother rushing in to help his sister. Mei remembers how Yohei used to be like that, but once he joined the football club he didn't seem to care about her any more. The group then tries to provoke a brotherly response from Yohei, to get him to stand up for his sister; Tomoya pretends to be romantically interested in Mei, but despite being shocked, Yohei doesn't say anything to oppose them. Mei decides to stay a little while longer, as she can't leave things the way that they are.

Youhei has not been coming to class lately, and his friends and Mei are worrying about his situation. Mei, Tomoya, and Nagisa visit the soccer club, and try to convince them to let Youhei rejoin. After a grueling task of fetching soccer balls, the club still will not let Youhei back on the team. While the leader of the soccer team makes Mei cry and picks on her, Youhei storms in and starts beating up the entire soccer club with the help of Tomoya. After the soccer team members leave, Tomoya and Youhei have another fight about the protection of Mei. Youhei finally admits he was worried about Mei, and the fight is resolved after Mei and Nagisa interject. Tomoya later recounts to himself how he and Youhei first met.

Tomoya tries to convince Akio to talk to him about his decision to marry Nagisa. Akio, however, will only talk to him if he can get a decent hit with a baseball match. Tomoya continues to practice hitting the ball until he gets good enough to face Akio again. He finally hits a home run, and runs over to Akio to beg him to let Nagisa be with him; Akio agrees. Christmas time arrives, and as Nagisa turns twenty, she has her first drink of sake; when she is drunk, she accuses Tomoya of being attracted to Sanae. Nagisa's fever goes up again, causing her to become absent from school, but not enough to repeat another year. Tomoya soon organizes with some of their friends and previous classmates to gather at the school and celebrate Nagisa's graduation. Nagisa receives her diploma and graduates. Tomoya and Nagisa get married soon after.