If there was no so-called organization, would we be happy? I know that I am not qualified to say this. Because it was the people in the organization who raised her and they taught her to understand the world.
Ai Haihara is Shirley Kiyabo, and Conan Edogawa is Shinichi Kudo. They were forced by a mysterious organization to take a drug that can shrink people. The story revolves around them and that mysterious organization.
There are some differences between the storyline and the anime, I hope comic fans don't mind.