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."

Kouta has girl troubles of the supernatural sort. For some reason, he keeps attracting the attention (and affections) of animal spirits! Having spent most of his life in the country, Kouta is understandably nervous when he moves in with his grandma to attend a high school in the big city. He hoped to make a good impression, but having Chizuru, a beautiful fox spirit, hanging off his arm didn't seem to be the sort of image he wanted to have. She's not alone in her love for Kouta, either. Nozomu, a wolf spirit, as well as other youkai have their sights set on the hapless country boy.

A young boy silently sketches out the forms of the horrors that dwell in his mind. During this adventure into the occult and mysterious, he tells tales that involve dreams of a person with a muscular arm that you must not look at, a hospital with a room that holds a grim secret, and a visit to an eerily silent taxidermy museum. These tales and more are compiled in Yami Shibai 3. Presented in an art style similar to kamishibai storytelling, this horror series stays true to the gruesome and creepy trend that is prominent in Yami Shibai and Yami Shibai 2nd Season. [Written by MAL Rewrite]

Excited children gather around the enigmatic masked Storyteller once more. His unique kamishibai storytelling draws them into tales of fear and dread. These are dark and foreboding stories, which could happen to anyone... This season has tales of a salaryman who buries a dead cat, only to be haunted soon after; a college student and her cheap new apartment that hides a ghastly secret; boys exploring an abandoned haunted house before coming across a strange fish tank; a man who finds himself on the wrong bus, and in more danger than he thought possible; and a young couple's visit to an amusement park, which suddenly takes a dark turn. All these stories and more await in Yami Shibai 4. [Written by MAL Rewrite]