Gin is a talented man. He could just be pretending to be two people. When Vermouth was first introduced, he seemed very fond of her(or they were just lovin trash talking about Pisco ;D). So he could still be the boss and is just placed himself in the field to be more aware of what his members are doing.Conan324 wrote: Actually......i always thought gin was the boss until 345
Another would be that Okiya is actually the boss and Conan is aware of this. Unlike his members, he was able to notice a strange coincidence from their reports to him of events and decided to investigate(because he now knows his members are idiots) the last lead. After seeing a little girl who resembles the escaped Shiho(pictures of the annual picnic), he turns on his vibe and Shio bites confirm it for him. With this, he immediately sees through Conan's ruse because it happens that the only person Shiho manually edited in the "APTX4869 death list" happened to be a famous High School Detective and this kid is doing a too good of a job on this case.
With all this settled, Okiya aka Boss, being a man of fun lets Conan knows what he just discovered. He drops the Holmes lines with Conan quickly equates to "It's finally nice to meet you Mr. Holmes, I am your Moriarty". This is why Conan knows he's not a "bad person"(aka he has principles and rules unlike some of his members) and Conan accepts his challenge by letting him stay at his house so they can play their game. Reason Conan knows that he isn't after his life or Sherry is because he could of walked away with his discovery without saying a thing and sent in Gin for clean up.
And finally, I'm not reading the manga but I did see a scan of a page where Okiya is at the mall and angry at Chianti. This makes people believe he's Akai or that Bourbon is angry Chianti but the truth is that it's just the boss showing his anger for his members because they seem to be making movements without his permission. So, once he's done with his little game, he will discipline all of them(and it's not going to be pleasant) and find out who the hell gave Bourbon permission to dress as Akai.
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