Eight years after the mysterious death of his father, Kaito Kuroba, a slightly mischievous but otherwise ordinary teenager, discovers a shocking secret: the Phantom Thief Kaito Kid—also known as The Magician Under the Moonlight—was none other than his own father. The former thief was murdered by a criminal organization seeking a mythical stone called the Pandora Gem, said to shed a tear with the passing of the Valley Comet that comes every ten thousand years. When the tear is consumed, the gem supposedly grants immortality. Vowing to bring those responsible for his father's death to justice, Kaito dons the Phantom Thief's disguise, stealing priceless jewels night after night to find the Pandora Gem before his enemies can use the power for themselves.

Fortune smiles on Inuyasha and his allies when they finally defeat their nemesis Naraku, who has caused them unrelenting hardships. Overjoyed by the long-awaited victory, they all hurry to resume their former lives, unaware that danger still lurks around. Kanna and Kagura, two of Naraku's subordinates, make arrangements to set free a sealed demonic entity that claims to be Kaguya, the legendary Princess of the Heavens. Although preoccupied with their own endeavors, Inuyasha's group members reunite by a string of unusual coincidences involving Kanna and Kagura along with an inexplicable phenomenon of repeated full-moon nights. Upon realizing that Kaguya is behind the troubling events and that she holds a terrible power, they join forces once more to stop the disastrous fate she has planned for the world.

Cursed by a witch, the feral and tempestuous Guideau tenaciously searches for the culprit so she can exact revenge. To this end, she joins the Order of Magical Resonance, an organization that deals with everything connected to magic. The Order agrees to work with Guideau in return for her help solving the myriad of magic-related cases occurring across the world. The Order's suave and mysterious mage Ashaf accompanies Guideau for the sake of successfully completing missions. As the pair traverses the land in search of that unknown witch, their experience with the fantastical world of magic grows ever more peculiar the further they advance in their journey.

The Shepherd, an urban legend of Shiomi Academy, is said to appear before hardworking students to grant them a wish. While engrossed in a book inside the school's renowned Great Library, Kyoutarou Kakei, a second year student and the Library Club's de facto president, receives an email from the Shepherd foretelling an event that will change his fate. Worried by the message, Kyoutarou rushes over to a nearby train station and encounters fellow student Tsugumi Shirasaki, whom he saves from being hit by a derailing train. Grateful for his heroic actions, Tsugumi joins the Library Club and invites Kyoutarou to participate in her mysterious Shiomi Happy Project. Together with other new members of the club, they strive to make the academy a better place and uncover the identity of the enigmatic Shepherd.