I get it! Agasa is the boss of the organisation and shrunk Shinichi so that Yusaku and Yukiko would give him some money to protect and help Shinichi and hence, he can corrupt part of the money. While he is doing this, his secret affair partner, Megure keibu, helps to cover the truth of the case. Every time an officer is about to solve it, he will move him or her to another case or department! hahaha....jk