One day, Jodie sees someone walking under an umbrella who looks like Shuichi.
The fingerprints on the phone Jodie gave to Takagi to check came back as being Conan's, Jodie's and the same prints as the ones from the body in the fire from the explosion that apparently killed Shuichi (The body and prints being Rikumichi's).
The "Akai" with burns on his face that Jodie sees, is actually Vermouth in disguise. She is helping Bourbon to see if Akai is really dead based on the reactions of those who see her in that disguise. (This is revealed in a later case that involves Vermouth and Bourbon on a train)
Gin Vodka and Candy follow the man that looks like Shuichi to that department store waiting to determine if it really is him, and if it is, kill Kir (and Akai) (because it would mean she only pretended to kill him(Akai) in the car fire, which would prove she's actually working with him)
This also shows that for some reason Vermouth is hiding what she's doing from the organization as well. And Bourbon is too, obviously because he isn't really one of them.
Gin talking to Rena asks if "he" knows about the situation at the department store. He is referring to Bourbon. He says that like Vermouth he is very secretive. But, Rena says that she heard that he is looking for that scientist who escaped the organization (Sherry/ Haibara).Then Vodka says that Bourbon hates Akai, even more than Gin does. Then Gin says that Bourbon didn't believe that Akai was dead from the beginning because he(Bourbon) thinks he's(Bourbon) the only one that could kill him(Akai).
Put simply, Bourbon and Vermouth are keeping their plans secret, even from each other for the most part.
