Due to a mysterious disease, the genius Iria Akagami has been forced by her family to stay in a mansion on the isolated Wet Crow's Feather Island with only a handful of maids. To keep herself entertained, Iria invites a variety of fellow geniuses to stay as guests in her home, including computer savant Tomo Kunagisa and her unnamed assistant, skilled fortune-teller Maki Himena, famous artist Kanami Ibuki, academic scholar Akane Sonoyama, and renowned cook Yayoi Sashirono. These visits progress as normal until one of the guests is found gruesomely murdered in the night without a single clue as to the identity of the killer or a possible motive. Tensions rise between those on the island as the killer remains at large, and Tomo's assistant takes it upon himself to uncover the culprit's identity before the murderous events progress any further.

In 2039, helper androids are widespread as general purpose electronics. Keiichiro lost his family in a traffic accident and retired from his band. One day, he finds an android of an old model in a garbage dump. He takes her home, but after taking her to a repair shop he was told that she couldn't be repaired, so he plans to throw her away. The next day, Keiichiro finds her making breakfast for him. Thus begin the summer days of an android with no memories and a dreamless boy.

Following an accident where Masato Inohara batted a baseball into the school's water main, the boys' dormitory is partially crippled. Until a plumber repairs the damage, the boys have to stay in the girls' dormitory. To determine which rooms they'll be assigned to, they draw tickets from a hat. Unfortunately, due to the limited capacity, some of the boys will have to go without a bed. Once Riki Naoe draws his ticket, he gets one that forces him to stay in one of the less-than-cozy clubrooms. Seeing his hapless predicament, a nervous Kudryavka Kud Noumi musters enough courage to confront her feelings while asking Riki to sleep in her room instead. Despite the rest of the Little Busters incessantly teasing Kud and Riki about their relationship, he stays with her throughout the summer. As they share unforgettable experiences one after another, the two realize that they might want to be more than just friends.

One fateful day, Youtarou Misaki is rescued by a man named Arashi Mutou from drowning in the sea. After getting him to dry land, Arashi wakes Youtarou up and asks for his name. Youtarou's memories quickly surge back, but instead of telling Arashi his name, he decides to lie and act clueless about his past. Arashi nurses Youtarou and lets him temporarily stay at his diner, Kurage no Shokudou. Despite his hospitality, Youtarou continues to insist that he has no recollection of how he ended up drifting across the sea. How will the fake amnesiac go on with his life now that he has abandoned his family and home?