Two years after the decisive battle with the Black Organization, Haibara joined the Tokyo National Research Institute as a genius girl and continued her research on APTX4869. But the good times didn't last. A confidential Tokyo Metropolitan Police Department file was stolen, officers were murdered, and the National Research Institute came under attack. A series of cases shattered the peace. To solve the crimes and compete for the results of the APTX4869 research, the Tokyo Metropolitan Police Department, the CIA, the FBI, mercenaries, and violent gangs were all drawn into the fray. Threatened by the opposing side, Haibara, once branded a "defector," was forced to flee again. This time, she was accompanied, as always, by the boy she had buried deep in her heart.