Three years ago, a gateway between Earth and the Beyond opened in New York City, trapping extradimensional creatures and humans alike in an impermeable bubble. After the city's restoration, monsters, magic, and madness are common findings in the area now known as Hellsalem's Lot. Leonardo Watch, a young photographer who unwillingly obtained the "All-seeing Eyes of the Gods" in exchange for his sister's eyesight, came to this paranormal city to find answers to the mysterious power that he possesses. He later finds his life drastically changed when he joins Libra, a secret organization of people with supernatural abilities dedicated to maintaining order in the everyday chaos of Hellsalem's Lot. However, this is only the beginning of Leonardo's unexpected journey ahead. Regardless of the constant threat of otherworldly enemies, he is determined to uncover the secrets of his power and find a way to restore his sister's eyesight. Kekkai Sensen & Beyond follows Leonardo as he sets off on more crazy adventures with his comrades, fighting to ensure peace and order.

Despite the kaleidoscopic magic ingrained in everyday life, Hitomi Tsukishiro's monochrome world is deprived of emotion and feeling. On a night as black and white as any other, amidst the fireworks spreading across the sky, Hitomi's grandmother Kohaku conjures a spell, for which she has been harnessing the moon's light for 60 years, to send Hitomi back in time to the year 2018 when Kohaku was in high school. Hitomi's mission seems unclear, but her grandmother assures her that she will know when she gets there. Following a trip through time aboard a train driven by a strange yellow creature, Hitomi finds herself in stoic artist Yuito Aoi's room, and his drawings flood her world with color. What is Hitomi's purpose there, and why do Yuito's drawings return such breathtaking color to her drab world?

In the town of Kurouzu-cho, Kirie Goshima lives a fairly normal life with her family. As she walks to the train station one day to meet her boyfriend, Shuuichi Saito, she sees his father staring at a snail shell in an alley. Thinking nothing of it, she mentions the incident to Shuuichi, who says that his father has been acting weird lately. Shuuichi reveals his rising desire to leave the town with Kirie, saying that the town is infected with spirals. But his father's obsession with the shape soon proves deadly, beginning a chain of horrific and unexplainable events that causes the residents of Kurouzu-cho to spiral into madness.

Mio has feelings for her childhood friend Arata, but can't convey her feelings. One day, as they continue their delicate relationship, the two fight over something trivial. After letting tensions settle, Mio goes to make up with him in the pouring rain. While on her way, she gets into a traffic accident. When she regains consciousness, a mysterious and unfamiliar world appears before her eyes.