One morning, Kyosuke is surprised to find Kirino behaving politely to him. That evening, while Kyosuke worries about whether she is forcing an act in front of everyone, Kirino uses her final life counseling session to ask Kyosuke to buy her an eroge that is launching at midnight in Akihabara. As Kyosuke gets in line, he runs into his classmate, Kōhei Akagi, who is buying a yaoi eroge for his own sister. Kyousuke, after realizing that the trains are no longer running, manages to convince one of the other customers to lend him his bike so he can ride back home. After Kyosuke gets back home with the game, Kirino asks him to play with her. She then shows him all of the medals and report cards with bad grades she had received throughout the years. The next morning, Kyosuke learns that Kirino has left home for America for track and field training. In the beginning of the new school term, Kyosuke meets up with Kuroneko, who would be attending his school as his underclassman.

Kuroneko (real name: Ruri Gokou) enrolls in Kyousuke's school, and Saori feels downhearted that she hasn't heard from Kirino. Kyousuke notices that Ruri is having trouble making friends due to her personality, so he decides they should try a membership at their school's Games Research club where the boy meets two other persons he never expected to be there as well.

With Sena and Kuroneko constantly quarreling in the Games Development club, the club president decides they'll have to write a game together and submit it to an online contest. Both girls have different concepts about the game's theme, so they'll both present them to the club whose members will then decide by majority vote whose concept will have to be implemented. And Kyousuke, with no programming skills thus acting as supervisor for the team, suggests to write an eroge—in order to have less competition and a better chance to win the contest.

As Ruri and Sena's game is bashed on the Internet they decide to work harder towards making a better game. As Kyousuke prepares to go home he receives a text message from Kirino telling him to throw away her collection of eroge and anime goods! Kyousuke contacts Ayase who confirms Kirino hasn't been in contact with her since she left either. Kyousuke then meets up with Ruri who encourages him to fly to America to find the root of Kirino's problem—and before the boy leaves she puts a special jinx on him.

Recap of the first episode, with additional comments from the characters.

Kyosuke meets with Ruri and tells her he loves someone else. The next day, Kyosuke asks Kirino out on a Christmas date to Akihabara like they did a year previously. Kyosuke reveals that he had finally fallen in love with a girl, which upsets Kirino and causes her to run off. Giving chase, Kyosuke quickly looses sight of Kirino when at that moment Kaori, Saori and Ruri show up in a minivan. After spotting Kirino, Kyosuke jumps out of the van and corners her. Not denying his feelings any longer, Kyosuke publicly acknowledges his love for Kirino. Kyosuke then asks her to stay in Japan and marry him. Kirino tearfully accepts.

Kyosuke gives Kirino a Christmas present which turns out to be the same ring she had asked him for the year previously. Kirino reveals that she had planned on confessing to Kyosuke herself. Kirino whispers to Kyosuke an idea for handling their relationship. Time passes and the siblings formally announce their relationship to Saori and Ruri. Later, Kanako confesses her love for Kyosuke which he rejects. The next morning, Kyosuke surprisingly wakes up with Kirino in his bed. Kirino reveals a photo album containing the memories they shared together while growing up. Kirino and Kyosuke listen to the diaries she had been recording since she was young.

Kyosuke and Manami graduate from high school. After the graduation ceremony, Kirino arrives to pick Kyosuke up following the end of her middle school graduation, and both head out to meet Manami. In a park, Manami scolds them about their relationship. Manami and Kirino then get into a fist fight. Manami scolds them some more and then confesses her love for Kyosuke. Manami then punches Kyosuke and accepts his rejection. Later on, Kirino and Kyosuke have a pseudo-marriage at the church. They kiss, and then Kirino gives Kyosuke back the ring she was given before. It's revealed that Kirino's idea for their relationship was to be a couple until graduation and then go back to being normal siblings. In the epilogue Kyosuke and Kirino head to Akihabara for a meet-up with Saori and a new member. Kyosuke casually kisses Kirino on her cheek, much to her disgust.

Special Included with Volume 4 of Season 2

Special Included with Volume 6 of Season 2