Seven years after humanity was devastated by a major disaster, a beacon of science and prosperity rises in Kamitsubaki City. But lurking in its shadows are Tesseractor, monsters born from human darkness. Only the Witchling, five girls with voices that wield magic, stand against them. With every note, they fight, not just to protect the peace of the city, but to heal a broken world.

At a CD store, Ichika Hoshino hears a song by Miku that she has never heard before. On the monitor, she sees a "Hatsune Miku" in a form she has never seen before, and couldn't help say it out loud, "Miku!?" Miku was surprised at the voice, her eyes meet Ichika's, but she disappears shortly after. Later, after a live performance on the street, the Miku that Ichika saw before appears on her smartphone. Miku looks sad and downcast, and when Ichika quietly asks Miku about her story, she tells Ichika that there are people to whom she wants to deliver her songs, but no matter how much she sings, her songs are not reaching them. Miku, who saw Ichika singing to the hearts of many people at her live performances, thought that if she learns more about Ichika, she can do the same, and came to Ichika. Ichika smiles at Miku and says, "If it's all right with me." And a new story of Hatsune Miku and the boys and girls begins—.

Middle school student Satomi Oka ought to be proud that his choir group placed second at a national competition. However, he views this achievement as a failure caused by his inadequacies. Furthermore, since graduation is fast approaching, his time as leader of the choir is coming to an end. While Satomi is preoccupied with his inner turmoil, a smooth-talking gangster named Kyouji Narita approaches him and requests him as a singing teacher. Every year, Kyouji and his colleagues participate in a karaoke competition, where their boss personally designs a tattoo for the loser. To avoid such cruel and unusual punishment, Kyouji asks Satomi to help him find the best song suited for his vocal range. Albeit reluctantly, Satomi sets his fears aside and agrees to join Kyouji at his karaoke practice sessions. But it remains to be seen whether the mismatched duo will overcome their respective obstacles or fail miserably.

Takeru Narihira is a lone wolf delinquent who spends his days getting into fights, avoiding friendships, and being captivated by a mysterious girl named Tsukimiya—someone he's only ever seen in his dreams. One day, a sudden accident sends him tumbling off a cliff. When he regains consciousness, he finds himself in Denji Heian-kyou, a futuristic version of the ancient capital, where advanced technology and mysticism coexist. This world is under the protection of the legendary onmyouji, Abe no Seimei—and to Takeru's shock, Tsukimiya is real and living in this very place. Just as he begins to revel in this fated encounter, a deadly black mist known as Yamikaoru descends, bringing forth monstrous beings called Oni. In the chaos, both he and Tsukimiya are killed—only for Takeru to awaken once again in Denji Heian-kyou. Realizing he has somehow slipped through time, Takeru resolves to defy fate. To protect Tsukimiya from her doomed future, he turns to Abe no Seimei to train in the art of onmyou-jutsu. Now, as an onmyouji himself, he must fight to rewrite destiny and uncover the truth behind this strange new world.