Fujimaru, his father, and his friends are trapped inside Mishiro Gakuin High School when the terrorists reveal they have a biological time bomb that threatens the entire city.
After J and his terrorist group release the Bloody-X virusin the basement of Third-i, Fujimaru is trapped, and his situation becomes more dire when he discovers that one of his allies has betrayed him.
Outwitted by the mysterious terrorist "J," Fujimaru is forced to defend the "Christmas Assassination" chip from terrorists seeking to reacquire it while stopping the spread of the "BLOODY-X" virus.
When THIRD-i holds his sister and best friend hostage in relatiation for his attempt to capture Hosho, Fujimara is forced to meet Hosho and Maya's demands to free his loved ones.
After Fujimaru detains Maya, Third-i is able to question her about the Bloody Monday plot. Meanwhile, Fujimaru is able to decode the two files Ryunosuke gave him and finds a commonality between the current terrorist plot and an incident from two years earlier.
The more he learns about the Bloody Monday terrorist plot, the more determined Ryunosuke becomes to expose the conspiracy, but more new questions arise than are answered, such as who K is and how Maya fits into the whole thing.
Fujimaru's investigation into the Bloody Monday data comes to a halt when the terrorists kidnap his sister and demand Falcon complete a hacking job for them in exchange for her safe return. With his sister in dire need of dialysis, Fujimara is desperate to find a way to save his sister quickly, but without assisting the terrorists' plot.
With the escape of terrorist leader K, Fujimaru and THIRD-i have only five days to prevent "Bloody Monday" from finally arriving courtesy of K's neutron bombs.
