In the witches' tradition, when a practitioner turns 15, they must become independent and leave their home to study witchcraft. Makoto Kowata is one such apprentice witch who leaves her parents' home in Yokohama in pursuit of knowledge and training. Along with her companion Chito, a black cat familiar, they embark on a journey to Aomori, a region favored by witches due to its abundance of nature and affinity with magic. They begin their new life by living with Makoto's second cousins, Kei Kuramoto and his little sister Chinatsu. While Makoto may seem to be attending high school like any other teenager, her whimsical and eccentric involvement with witchcraft sets her apart from others her age. From her encounter with an anthropomorphic dog fortune teller to the peculiar magic training she receives from her older sister Akane, Makoto's peaceful everyday life is filled with the idiosyncrasies of witchcraft that she shares with her friends and family.

On Christmas Eve, Hiro Hirono runs into Miyako Miyamura, a frivolous girl who borrows his bicycle in order to chase down a purse thief. After Hiro finds his bicycle wrecked and Miyako unconscious, the two unexpectedly spend their Christmas Eve together, and when they discover they go to the same high school, their accidental relationship develops even further. This sparks the jealousy of Hiro's childhood friend Kei Shindou, whose pure approach to life catches the eye of Kyosuke Tsutsumi, a womanizing photographer searching for the perfect shot. Elsewhere, Renji Asou, a boy who dreams of being a girl's knight in shining armor, has a chance encounter with Kei's twin sister—the overly shy Chihiro Shindou, who spends her time reading alone—at an abandoned train station. The two quickly become friends and eventually decide to write a novel together. However, when Renji discovers Chihiro's secret, his childish ideals are put to the test. Guided by two mysterious adults, these youths' relationships intertwine in a heart-rending tale of love, rejection, acceptance, and memories.

Continuing his adventure to get stronger in order to traverse deeper into the Dungeon, Bell Cranel wanders the Orario city streets with his friends and the goddess Hestia. That evening, the city is filled with stalls and games as it celebrates the Holy Moon Festival. Hermes, a god, hosts one such activity where participants are asked to pull a spear embedded in a crystal boulder; those who succeed will receive a special gift: a trip around the world and a divine blessing from the gods! Bell and his merry group challenge one another to claim the prize. But behind the facade of an innocent party game lies a preface for a daring quest ahead.

Soul Eater NOT! is a spin-off and side story that takes place one year prior to the events of the original Soul Eater. At the Death Weapon Meister Academy, humans born with the power to transform into weapons and those with the power to wield these weapons (Meisters) train to hone their natural talent. The characters of the main series are enrolled in the Especially Advantaged Talent class, where they train to become warriors of justice capable of defeating what threats prey on innocent lives—or even the entire world. Other students at the DWMA are less talented. Members of the Normally Overcome Target class focus less on being warriors of justice and more on controlling their powers so they don't hurt themselves or anyone around them. Tsugumi Harudori, a new halberd-transforming student, meets Meisters Meme Tatane and Anya Hepburn and quickly grows indecisive about which of the two new friends should be her partner. As they learn to use these powers and settle in, their lives as everyday students will be far from normal.