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.

As a child, Riki Naoe shut himself from the world, thanks to a diagnosis of narcolepsy following the tragic deaths of his parents. However, Riki is saved when, one fateful day, a boy named Kyousuke recruits him into a team who call themselves the Little Busters. Accompanied by Masato, Kengo, and Rin, these misfits spend their childhood fighting evil and enjoying their youth. Years pass, and even in high school, the well-knit teammates remain together. Kyousuke decides to re-ignite the Little Busters by forming a baseball team as it will be his last school year with them. They have a problem though: there aren't enough members! The tables have turned, for it is now Riki's turn to reach out and recruit new friends into the Little Busters, just like Kyousuke had once done for him. Then, an omen surfaces—Rin finds a strange letter attached to her cat, assigning them the duty of uncovering the secret of this world by completing specific tasks. Just what is this secret, and why is it being hidden? It's up to the Little Busters to find out!

The main additions in Little Busters! Ecstasy are 3 heroine routes involving the characters Futaki Kanata, Sasasegawa Sasami and Tokido Saya. The 3 EX heroines' routes take place of the following: Saya's route - Before the events of Refrain. Sasami's route - After the events of Refrain. Kanata's route - First half of her story is before Refrain and second half is after Refrain. The episodes will be bundled with the BD/DVD releases of Little Busters!: Refrain.

Suzuko Homura and Chinatsu Morikawa's victory against the nefarious Bookmaker Kou Satomi has allowed the two girls to finally return to a life of normalcy and seize the chance to move on. However, the peace does not last long, as Kiyoi Mizushima requests Suzuko's help to prevent the next cycle of Selector battles; even after Satomi's defeat, efforts to continue his plans seem to persist. Troubled by lingering doubts and the unresolved situation, Suzuko decides to assist Mizushima with her investigation—unknowingly becoming involved in the escalating fight that will determine the fate of Selectors once and for all.