Tomoya realizes that he met Kotomi as a kid, though only she had remembered. Back then, Tomoya had often visited Kotomi, and was her only friend. Around this time on Kotomi's birthday, her parents left for business reasons, and later that day she finds out they were killed in a plane crash. Kotomi ultimately ended up burning her father's important work before anyone could see it. While Kotomi shuts herself in her house, Tomoya comes over and starts cleaning up the garden which is overgrown with grass and weeds. Nagisa, Kyou and Ryou eventually help out too.

Kotomi finally leaves the house to find that Tomoya worked in the garden all night long and had fallen asleep. When she returns to school, Tomoya, Kyou, Ryou and Nagisa are all waiting for her. The mysterious stranger whom she was so frightened of, believing he wanted to steal her parents' thesis, is there as well. Kotomi and her friends find out that he is her legal guardian, and that there never were any written notes for the thesis after all. The envelope Kotomi set fire to, and felt so guilty about, was nothing important. The stranger also has a birthday gift for her: her parents' suitcase, which survived the plane crash and was passed from hand to hand for years until he found it. Inside is a teddy bear, Kotomi's gift request to them before they left, and an affectionate letter. Kotomi, holding the bear, is so happy that sparkles literally fill the room, and makes peace with her parents' deaths at last.

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.

After watching the basketball game, the choir club decides to share Koumura with the drama club, but the student council will not allow it. Nagisa collapses at school and cannot come to school for a few days. During this time, Tomoyo starts waking up Tomoya and Youhei before classes start so they will not be late anymore. Kyou continues to set up situations where Tomoya and Ryou are together, such as eating lunch together. Yukine tries to help Tomoya with a charm book, and he performs a charm to get locked in the gym equipment room with Kyou, which ends up happening. Kyou does not act like her usual self while in the room, and thinks that Tomoya may end up trying to have sex with her. Tomoya undoes the charm and the door is opened by one of Kyou's classmates. Tomoya and Tomoyo start to walk home after school, but a a bunch of gang members are at the school's entrance looking to fight Tomoyo.

During the time that Tomoya is suspended from school, Tomoyo continues to come to his house, wake him up, and make him breakfast, though when she tries to ask him about his relationship with his father, he does not answer her. On Sunday when Tomoyo is making him lunch, Kyou, Ryou, and Kotomi arrive each bringing a bunch of food, and even Fuko appears with food; Tomoya ends up eating everything. Once back at school, he finds out how Tomoyo's reputation is dropping due to rumors of her as a gang leader, and arranges for Tomoyo to compete against several school sports clubs to boost her reputation. After school, Tomoyo tells Tomoya about her family situation and how her brother risked his life to keep their parents from divorcing. Nagisa finally comes back to school and is welcomed by her friends. During a tennis match between Tomoyo and a male tennis club member, a stray ball hits Nagisa on the leg, and Tomoya overprotects her, showing everyone how devoted he is to her.

The drama club is finally re-established and Koumura is shared with the choir club. Tomoya's home room teacher goes to Tomoya's house to ask his father about his future, but Tomoya's father says that is something that Tomoya has to decide for himself. Seeing the strained relationship between Tomoya and his father, Nagisa offers to have Tomoya stay over at her house for the time being, which he accepts. After coming home from school, Tomoya finds several small kids in Nagisa's house, and finds out Sanae is instructing them in a cram school. Nagisa confides to Tomoya that she feels she did something really bad to her parents in the past, but she cannot remember what it is, and her parents say that she must be imagining it.

After hearing Nagisa talk about the story for the play she wants to perform, Tomoya tries asking Nagisa's parents about it, but they do not know any story like that. After Akio catches Tomoya and Nagisa in the shed, he tells them to leave, and later brings Tomoya aside to tell him about what happened in the past. Ten years prior, Nagisa was running a high fever one snowy day, and in the midst of this, her parents had to work, so they left her alone for a couple of hours. When Akio returned, he found Nagisa collapsed outside as she had been waiting for them to return. Due to Nagisa nearly dying, both of her parents abandoned their jobs and their dreams in order to protect Nagisa. Akio tells Tomoya not to tell either Sanae or Nagisa about the story since he does not want it coming up again. Tomoya goes on a picnic with Nagisa's family, and during a baseball game with some local young boys, Nagisa accidentally confesses her love to Tomoya indirectly.

Nagisa and her friends continue to practice for the play, such as reciting tounge twisters, choosing which music to use for the play, lighting, and stage direction. Nagisa's father rents a play on video, and Nagisa finds it very touching, plus it was the first play she ever saw. Tomoya and Akio try to find the script of the play that Nagisa is going to perform in the shed, but do not find it. The drama club has a practice the day before the school festival is to begin and it goes well. The night before the school festival, Nagisa looks for a flashlight in the shed, but bumps into some boxes and discovers photographs and diaries of her parent's pasts.

After Nagisa finds out about her parents' secret past, she cannot take her mind off how she ruined their dreams, and becomes emotional and depressed. On the day of the school festival, the whole theater club realizes that Nagisa is not herself, and try to cheer her up, but to no success. As the performance starts, Nagisa breaks down, but with encouragement from Akio, who said that Sanae's and his dream was for Nagisa to make her dream come true, the play was a huge success. The next day as the sun is setting, Tomoya finally confesses his love to Nagisa in the club room. This comes as a shock for Nagisa, causing her to cry tears of joy.

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.

In an alternative timeline where Tomoya and Tomoyo are dating, Tomoyo becomes student council president, but bad rumors start around the school due to Tomoya's bad reputation. Tomoyo becomes busy during the school festival, and continues to be so while she attempts to save the sakura trees in town. Tomoya realizes that he is holding Tomoyo back from greater things, and despite both sides being reluctant, they break up. Time passes as Tomoyo's reputation builds and Tomoya and Youhei watch on the side through her many accomplishments, one of them being ultimately saving the sakura trees by the winter. At that time, Tomoya and Tomoyo meet and talk for the first time in months and they decide to become a couple again.