The narrative begins by establishing a world irrevocably changed on May 25, 2020, when black hole-like spatial distortions appeared globally, unleashing monstrous creatures known as "Phenoms." These beings, ranging from colossal insects to fanged canine-like creatures and giant birds, caused widespread devastation, leading to the death of one-third of humanity. Humanity's initial military response was met with heavy losses, with only six nations managing to repel the Phenoms effectively.
In 2025, a turning point occurred with the emergence of individuals possessing special abilities called "Gifts," who became known as "Specialists." These Gifts manifested before the age of fifteen and provided humanity with the means to fight back. By 2050, humanity faced its greatest challenge: the "Unknown," a progenitor Phenom of immense power. A desperate battle ensued between 100 elite Specialists and 1000 Phenoms, resulting in the Unknown's defeat but at the cost of all but ten Specialists. While the dimensional rifts producing Phenoms shrunk, they did not disappear, continuing to spawn lower-level threats.
Twenty years later, in April 2070, the story focuses on Suou Kouki, a seemingly ordinary 17-year-old high school student in Neo-Tokyo's Minato Area. Kouki lives a mundane life, believing himself to be unremarkable and, crucially, without a Gift. The chapter arc begins on the first day of his second year of high school. He witnesses news of the "Nature Strangers," a popular Specialist unit of the National Defense Force, defeating a Phenom. The narrative then delves into the world's structure: the National Defense Force and the Police, both employing Specialists. It also introduces the concept of "Filth," rogue Specialists who misuse their Gifts, posing a threat alongside Phenoms. Kouki harbors a deep-seated desire to be a Specialist, driven by a longing for admiration, but his Gift-less status has left him apathetic and disillusioned.
Kouki's ordinary morning is interrupted by a collision with Mizutani Fuuka, a beautiful transfer student. Despite the encounter, his childhood friend, the charismatic and popular Sanada Hiro, immediately captivates Fuuka. At school, Kouki is assigned to a class for those without Gifts. He reconnects with his eccentric childhood friend, Matoba Takahiko, whose Gift, "God Eye," allows him to gather vast amounts of information. Takahiko reveals that several girls, including the formidable Yoshida Narumi, are interested in Kouki, but Narumi has been aggressively deterring any potential rivals. This revelation, coupled with Hiro's effortless charm and his own lack of a Gift, intensifies Kouki's feelings of inadequacy.
Later, Kouki shares lunch with Fuuka, who offers him half of her homemade bento. Their peaceful moment is shattered by the arrival of Narumi and three other physically imposing girls, who declare themselves Kouki's "Chastity Guardians" and warn Fuuka away. Hiro intervenes, revealing himself to be a Specialist with the "Area Master" Gift, capable of manipulating objects within his sight. He easily incapacitates the girls, much to Kouki's dismay, as he feels his own dreams of heroism slipping away.
That evening, Kouki, consumed by despair and jealousy over Hiro's success, engages in street fights, using his martial arts training to vent his frustration. He is confronted by a group of thugs and their leader, a man named Kurosaki, who reveals himself to be a "Rogue Filth" and a former military man. Kurosaki easily defeats Kouki, breaking his arm and leaving him for dead. However, Kouki's near-death experience triggers the manifestation of two Gifts: "Revive Hunter," allowing him to resurrect, and "Speed Star," an acceleration ability.
Kouki, now a Specialist, attempts to test his new abilities but struggles to control them. He is then confronted by Kurosaki, who is surprised Kouki survived. Kouki, empowered by his new Gifts, manages to defeat Kurosaki. However, his victory is short-lived as he is apprehended by Saejima, a National Defense Force Lieutenant, who mistakes him for a Rogue Filth due to the absence of a Specialist barcode. Kouki attempts to escape, using his Speed Star ability, and is pursued by Saejima. He seeks refuge in an abandoned factory, where he encounters Hiro and his superior, Kashiwagi. Hiro, now a member of the National Defense Force, uses his Area Master Gift to incapacitate Kouki, revealing a cynical view of the military and a resentment towards Kouki's past perceived passive acceptance of Hiro's successes. Kouki, despite his injuries and inability to communicate, realizes the harsh reality of the world and the true nature of the organization he once admired.