Kirino Kousaka has returned home and is now living with her friends and family in Japan. Although Kyousuke had previously helped her in many ways, Kirino continues to give him a cold shoulder, causing frustration for him. He worries that his persuasion for Kirino to drop her track and field training in America and return home may have damaged their relationship. Additionally, Kyousuke must decode a mysterious message from Ruri "Kuroneko" Gokou, one of Kirinos friends and classmates at school. As the bonds between the siblings and their companions grow stronger, Kirino and Kyousuke will need to determine how they want to handle these relationships while also understanding their own emotions. Despite this, Kirino still makes time for her otaku hobbies with the help of her brother.