The world of Lingalind is surrounded by a mystical wall with seemingly nothing beyond its confines. Worshipped as the mother of the land, the wall delivers celestial gift capsules called "Rakuho'' to locations across the continent. Arriving once a month, the capsules contain metallic armbands that allow the wearer to transform into a mechanical being known as a "Briheight." As a result, Lingalind is thrown into constant turmoil by its warring nations, all hoping to strengthen their military prowess by procuring the offerings for themselves. One day, a Rakuho crash-lands in the countryside with an unexpected inhabitant—a mysterious black-haired man. All eyes are set on this strange newcomer, who calls himself "Back Arrow," when he claims to have hailed from a place beyond the wall—a revelation that can potentially unravel Lingalind's entire dogmatic foundation.

At True Cross Academy, Rin Okumura unknowingly comes across the first signs that something is amiss; ordinary people have been gaining the ability to perceive the invisible creatures that roam the human realm, Assiah. While Rin sees this as an opportunity to make a new friend, his twin brother, Yukio, is more burdened than ever. Swamped with his education, exorcist duties, and teaching position, Yukio has remained silent about his awakened powers, unable to understand their scale or significance. While Rin and his friends prepare for the annual Exorcist Certification Exam, the True Cross Order has uncovered the first artificial gate to the demonic realm of Gehenna. Witnessing its size and the advanced technology that made it possible, the exorcists realize they are now dealing with the Illuminati, an extremely wealthy and powerful organization. Moreover, the inscrutable Illuminati have planted three spies in the True Cross Order—and one may be hiding among the aspiring exorcists sworn to protect mankind from the demonic threat.

The aloof protagonist: a bookworm who is deeply detached from the world he resides in. He has no interest in others and is firmly convinced that nobody has any interest in him either. His story begins when he stumbles across a handwritten book, titled Living with Dying. He soon identifies it as a secret diary belonging to his popular, bubbly classmate Sakura Yamauchi. She then confides in him about the pancreatic disease she is suffering from and that her time left is finite. Only her family knows about her terminal illness; not even her best friends are aware. Despite this revelation, he shows zero sympathy for her plight, but caught in the waves of Sakura's persistent buoyancy, he eventually concedes to accompanying her for her remaining days. As the pair of polar opposites interact, their connection strengthens, interweaving through their choices made with each passing day. Her apparent nonchalance and unpredictability disrupts the protagonist's impassive flow of life, gradually opening his heart as he discovers and embraces the true meaning of living.

Narumi Katou is a middle-aged man who suffers from the bizarre ZONAPHA Syndrome: a rare and inexplicable disease that causes its victims to endure severe seizures at random, with the only cure being to watch someone laugh. One day, during Narumi's part time job, a young boy with a giant suitcase fleeing from three adults runs into him. The boy introduces himself as Masaru Saiga, the new owner of the famous Saiga Enterprises following his father's recent death. However, other members of his family are trying to assassinate him and claim the fortune for themselves. Determined to save the child, Narumi helps Masaru escape and ends up fighting the pursuers, only to discover that they are sentient humanoid puppets with superhuman strength. As Narumi is about to lose, a white-haired girl suddenly joins the fray and swiftly summons yet another puppet from the boy's suitcase, claiming herself to be Shirogane, Masaru's guardian. Karakuri Circus follows three people from different backgrounds whose fates intertwine and diverge as they unravel the mysteries of an ancient tale of love and betrayal, and the long, ancient battle between humans and puppets.