On the hot summer day of August 14, Shintarou Kisaragi is forced to leave his room for the first time in two years. While arguing with the cyber girl Ene who lives in his computer, Shintarou Kisaragi accidentally spills soda all over his keyboard. Though they try to find a replacement online, most stores are closed due to the Obon festival, leaving them with no other choice but to visit the local department store. Venturing outside makes Shintarou extremely anxious, but the thought of living without his computer is even worse. It's just his luck that on the day he finally goes out, he's caught in a terrifying hostage situation. Luckily, a group of teenagers with mysterious eye powers, who call themselves the Mekakushi Dan, assist Shintarou in resolving the situation. As a result, he is forced to join their group, along with Ene. Their abilities seem to be like pieces of a puzzle, connecting one another, and as each member's past is unveiled, the secret that ties them together is slowly brought to light.

Humans have designed countless worlds—each one born from the unique imagination of its creator. Souta Mizushino is a high school student who aspires to be such a creator by writing and illustrating his own light novel. One day, while watching anime for inspiration, he is briefly transported into a fierce fight scene. When he returns to the real world, he realizes something is amiss: the anime's headstrong heroine, Selesia Yupitilia, has somehow returned with him. Before long, other fictional characters appear in the world, carrying the hopes and scars of their home. A princely knight, a magical girl, a ruthless brawler, and many others now crowd the streets of Japan. However, the most mysterious one is a woman in full military regalia, dubbed Gunpuku no Himegimi, who knows far more than she should about the creators' world. Despite this, no one knows her true name or the world she is from. Meanwhile, Souta and Selesia work together with Meteora Österreich, a calm and composed librarian NPC, to uncover the meaning behind these unnatural events. With powerful forces at play, the once clear line between reality and imagination continues to blur, leading to a fateful meeting between creators and those they created.

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.

During a Literature Club meeting, the four club members—along with their faculty adviser's niece—suddenly find themselves with supernatural powers. Now capable of fabricating black flames, resident chuunibyou Jurai Andou is the most ecstatic about their new abilities; unfortunately, his own is only for show and unable to accomplish anything of substance. Moreover, he is completely outclassed by those around him: fellow club member Tomoyo Kanzaki manipulates time, Jurai's childhood friend Hatoko Kushikawa wields control over the five elements, club president Sayumi Takanashi can repair both inanimate objects and living things, and their adviser's niece Chifuyu Himeki is able to create objects out of thin air. However, while the mystery of why they received these powers looms overhead, very little has changed for the Literature Club. The everyday lives of these five superpowered students continue on, albeit now tinged with the supernatural.