Somewhere in Vladivostok, Russia, a deal has been successfully completed. Danger looms over the horizon; a deadly virus—capable of killing within three hours of infection—has now fallen into the hands of a mysterious woman named Maya.

Enter Fujimaru Takagi, a seemingly ordinary student at Mishiro Academy in Japan. However, very few know that he was famed for exposing crimes and corruption of high-profile individuals with his brilliant hacking powers—the infamous "Falcon" who had abruptly vanished from the cyberworld. Only members of Third-I, a top-secret division of the Public Security Intelligence Agency led by Fujimaru's father, Ryunosuke, and his friend Otoya Kujou know of his past.

When a KGB agent is murdered in Japan, the only clue to his death is a memory chip found at the scene of the crime. Fujimaru is recruited by Third-I to decode the chip, which contains a video file of an event called the "Christmas Massacre." Investigating the incident further, Fujimaru's father uncovers more information about the homicide and a mysterious code, "Bloody Monday," before being framed for the murder of his superior. Now, it is up to the hacker Fujimaru to utilize his expertise to help Third-I prevent the spread of terror and destruction in Japan, while attempting to clear his father's name.