Mushi-uta is set in the near future and begins ten years after the emergence of "Mushi," insect-like creatures capable of consuming people's thoughts and dreams in exchange for supernatural powers. As the story unfolds, Daisuke "Kakkou" Kusuriya befriends Shiika Anmoto, a young girl who unbeknownst to him, has escaped from GARDEN, a secret prison for those possessed by Mushi, known as the Mushitsuki. GARDEN's military, the Special Environmental Conservation Executive Office, sends their best assassin to track down Shiika, but they encounter resistance from the Mushibane organization led by the enigmatic "Ladybird."