Supersonic monkeys, vampires, talking fishmen, and all sorts of different supernatural monsters living alongside humans—this has been part of daily life in Hellsalem's Lot, formerly known as New York City, for some time now. When a gateway between Earth and the Beyond opened three years ago, New Yorkers and creatures from the other dimension alike were trapped in an impenetrable bubble and were forced to live together. Libra is a secret organization composed of eccentrics and superhumans, tasked with keeping order in the city and making sure that chaos doesn't spread to the rest of the world. Pursuing photography as a hobby, Leonardo Watch is living a normal life with his parents and sister. But when he obtains the "All-seeing Eyes of the Gods" at the expense of his sister's eyesight, he goes to Hellsalem's Lot in order to help her by finding answers about the mysterious powers he received. He soon runs into Libra, and when Leo unexpectedly joins their ranks, he gets more than what he bargained for. Kekkai Sensen follows Leo's misadventures in the strangest place on Earth with his equally strange comrades—as the ordinary boy unwittingly sees his life take a turn for the extraordinary.

One summer, Norimichi Shimada and his friends want to know if fireworks look round or flat from the side. They forge a plan to find the answer at Moshimo Festival's fireworks display. However, Norimichi finds himself conflicted when his classmate, Nazuna Oikawa, plans to run away from home and wants Norimichi to join her. When things go awry in their attempt to escape, a strange orb in Nazuna's possession gives them another chance at staying together.

Since the death of his parents, Shinpei Ajiro had lived with the Kofune family and their two daughters—Mio and Ushio. Although he then left his home island to continue his education in Tokyo, Shinpei returns after Ushio tragically drowns during the attempted rescue of a little girl. During the funeral, his best friend informs him about bruises found around Ushio's neck, casting doubt over the cause of her death. Suspecting a murder has taken place, Shinpei reevaluates recent events, but strange incidents only continue to transpire. Disappearing people and other unexplainable occurrences lead Mio to recall an old folktale referring to entities called "Shadows," which may not be entirely fantasy. Supposedly, an encounter with one's Shadow foretells the person's impending demise. Facing the dark side of Hitogashima Island, Shinpei stands against his grim fate to fulfill Ushio's final will—to protect Mio.

Novice bounty hunter Chateau Dankworth never expected to encounter someone capable of overpowering her in combat. Even less so that the mysterious man would take an immediate interest in her—to the point of aiding her missions. However, Chateau makes it clear that she has no plans of entertaining any personal involvement with him. Chateau's company is soon tasked with eliminating Song Ryang-ha—an expert assassin and a former member of a powerful Asian organization. Coincidentally, Ryang-ha is the man that has been pursuing her. Despite his background, Chateau reluctantly agrees to meet with Ryang-ha as part of a deal: in exchange for going out with him, he will provide her with the locations of current targets, dead or alive. But when the past begins to haunt both killers, their arrangement may need to come to an end, as their entanglement puts their lives at grave risk.