The story follows Risa, a girl with zero experience in romance. Meanwhile, a boy named Yuugure is the most popular student in Risa's school year. Even though the two have had no contact with each other in the past, they find themselves at school at the same time one night.

Mushi-uta's story takes place in the near future. Ten years before the story's opening, strange insect-like creatures known as "Mushi" began appearing. The Mushi are able to consume peoples' dreams and thoughts in return for supernatural powers. At the end of episode one, protagonist Daisuke "Kakkou" Kusuriya encounters a young girl named Shiika Anmoto. The two, in time, become quite close. However, unbeknownst to Kakkou, Shiika is an escapee from a secret prison known as GARDEN where those posessed by the Mushi, known as the Mushitsuki are held. GARDEN's military force, the Special Environmental Conservation Executive Office, dispatches its finest killer to track down Shiika. However, they are faced with resistance from the Mushibane resistance organisation, led by the secretive "Ladybird."

A side story that reveals the investigative notes that Atsuko, the younger sister of the main character Akihiko Chuzenji, wrote about the brutal dismembering incidents in the main story. (Source: ANN)

U.C. 0097, one year after the opening of "Laplace's Box." Despite the revelation of the Universal Century Charter that acknowledges the existence and rights of Newtypes, the framework of the world has not been greatly altered. The conflict later dubbed the "Laplace Incident" is thought to have ended with the downfall of the Neo Zeon remnants known as the Sleeves. In its final battle, two full psycho-frame mobile suits displayed power beyond human understanding. The white unicorn and the black lion were sealed away to remove this danger from people's consciousness, and they should now be completely forgotten. However, the RX-0 Unicorn Gundam 03, which disappeared two years earlier, is now about to show itself in the Earth Sphere once more. A golden phoenix... named Phenex.