Following the Little Busters after they lost their first baseball game, the team decides to have a pancake party. It has been almost one semester since the return of Kyousuke Natsume. As usual, Riki Naoe continues to help the Little Busters' members—both old and new—with confronting their inner struggles. However, strange happenings begin to occur, leading Rin Natsume and Riki closer to unraveling the truth behind the "secret of this world." Little do Rin and Rikki know, their discovery will end up changing the peaceful everyday lives created by the Little Busters once and for all. Little Busters!: Refrain brings a conclusion to the colorful stories of its ensemble cast—forged with the weight of emotions and strengthened with the bond of friendship—as they come to terms with their regrets and weaknesses. [Written by MAL Rewrite]

Corruption looms over the prosperous Russell City, where manifestations of negative emotions called Horrors cause chaos and mayhem. The Makai Order is the last bastion of hope against these unholy creatures. Using several small businesses as fronts, they deploy powerful Makai Knights and magical Makai Alchemists to combat the Horror threat. Within this secretive order, the highest rank of Golden Knight has been bestowed upon a large, powerful man named Sword, granting him use of the Garo armor and blade. He alone knows of a plot that threatens the entire Makai Order, with his only hint being the phrase “El Dorado." While fighting a Horror, he encounters Sophia "Sophie" Hennis, a teenage girl whose brother's disappearance years ago is also linked to the same phrase. The two agree to work together to uncover the truth behind "El Dorado" and the disappearance of Sophie's brother. [Written by MAL Rewrite]

Kanna loses her love of running after her mother passes away. Due to the workings of the gods, she heads to Izumo City.