A long time has passed since the original events of SHUFFLE! The worlds once trembled on the brink of destruction, a disaster threatening to rend the fabric of all existence. However, equilibrium was eventually restored, and with time, people moved on, relegating the memory of the catastrophe to the annals of history. At the dawn of another early summer, we turn the page to our new protagonist, Raito Aioi. Raito shares his home with his cousin, Kohaku Anjou, and their days are filled with the tranquillity of ordinary life. This peace, however, is abruptly disrupted when two princesses, Lithia of the gods and Nelia of the demons, enter Raito's life. Both girls enroll in Verbena National Academy, the same institution Raito attends. Lithia boldly proclaims her purpose: "I am about to sever the ties between gods and humans." On the other hand, Nelia smirks and issues a chilling threat: "I am here for your life." After these upheavals, Raito is now known as the "man targeted by god and demon." The sudden appearance of Limes, a chance acquaintance, adds another layer of complexity to Raito's life when she decides to move into his home. Moreover, Kirara Kinoshita, a junior who looks up to Kohaku, also becomes part of the increasingly dynamic equation. Raito's once-ordinary life has become an exciting whirlwind of events. As he spends time with these girls, he gradually uncovers the secrets they have been guarding in their hearts.