Arata Kokonoe, known almost exclusively by his code name Nine, is a 17-year-old young man and one of the two central figures behind the mysterious terrorist group Sphinx. He and his partner, Twelve, are survivors of a clandestine government project known as the Athena Plan, which sought to turn gifted orphaned children into human weapons. Using the alias Arata Kokonoe to blend into society, he enrolls in a Tokyo high school while orchestrating a series of elaborate public bombings designed not to kill, but to force the world to confront the hidden crimes of the institution that exploited him.

Physically, Nine is tall with an average build, black hair cut short with bangs that reach his eyes, and a gaze that is often described as grey or black. He typically wears dark, simple clothing and is seldom seen without a pair of dark blue-framed glasses, which he only loses near the conclusion of his story. His outward demeanor is one of profound stoicism; he is stern, aloof, and composed, rarely displaying emotion. This calm surface, however, masks a deep well of trauma and vulnerability. Nine is haunted by recurring nightmares of the fire he and Twelve started to escape their captivity, during which he was forced to leave behind another child, Five. Under extreme duress, such as when Five reemerges to hunt them, this emotional instability breaks through his stoic facade, leading to visible panic attacks.

Despite his criminal actions, Nine operates under a strict personal code. While he uses explosives and hacking to create chaos, he meticulously plans each attack to avoid civilian casualties, even going so far as to shield an innocent person from a blast. His motivations are neither greed nor malice, but a calculated, desperate attempt at revelation. He aims to expose the crimes of the Rising Peace Academy and the Athena Plan, using the Sphinx riddles as a public stage to force the police and the government into a game of wits they cannot ignore. In this partnership, Nine serves as the brains to Twelve’s more impulsive brawn, devising ingenious schemes and demonstrating exceptional computing, hacking, and strategic skills. He also possesses a remarkable ability to visualize spaces and objects in his mind with perfect clarity, allowing him to guide others through complex bomb placements or mentally reconstruct a chessboard to solve a puzzle.

His key relationships define the course of his life. His bond with Twelve is the core of his existence; they are childhood friends, co-conspirators, and the only family each other has left. Towards Lisa, a lonely girl who becomes entangled with them, Nine is noticeably more distant and less caring than Twelve. This coldness likely stems from a desire to protect her by keeping her at arm's length from the deadly consequences of their mission. His most fraught relationship is with Five, a former test subject from the Athena Plan who now works with American intelligence to hunt him. He harbors a complex mix of hatred and guilt for her, having left her behind during their escape. Her eventual death surprises him, revealing that his feelings for her are more complicated than simple animosity.

Throughout the story, Nine is forced to confront the limits of his control. The arrival of Five turns their careful game into a deadly and chaotic contest, exposing his emotional fragility. Ultimately, the physical toll of the drugs administered during his childhood in the Athena Plan proves fatal. He succumbs to the same debilitating headaches that plagued Five, a symbolic end for the mastermind of Sphinx. In his final act, he succeeds in his primary goal: detonating a stolen atomic bomb in a high-altitude electromagnetic pulse (EMP) attack that, while harmless to people, destroys Japan's electronic infrastructure and forces the truth of the Athena Plan into the open.