Alright, these are my suspicions:
First, I don't want to suspect a lot of the characters who are close to Shinichi, so basically anybody who has helped him (I'm not a fan of backstabbing I guess ). So I refuse to suspect Agasa! I even refuse to suspect Ran's mom.
So here's my guess: Haibara's mom or dad. If i had to guess between the two I'd guess her dad.
My reasoning:
-Haibara will be suprised by the boss's identity. I HOPE she would be suprised to find out here mom/dad is not only alive but running the BO. I also suspect this since it was mentioned only "Haibara would be suprised", possibly indicating Conan wasn't suprised (However Conan could have already deduced as much so he wouldn't be suprised).
-The boss is somebody introduced to the series already. Although only mentioned, Haibara's parents were in fact 'introduced'.
-This kind of twist is something I would expect the author to do to the series, it also seems like a good way to disapoint as minimal fans as possible without introducing a new character.
Reasons against my deduction: (lol DC is making me talking like a wanna-be detective )
-Haibara's parents are supposed to be dead. Ok, well this is the most obvious reason against my theory; but I mean c'mon! Somebody using a trick to fake their own death? Not even close to impossible in the world of DC.
-Would Haibara's parents target/kill their own daughter (Haibara/her sister)? Well ok let's think about this based on personality. Take Gin for example, a ruthless killer who will attempt to silence anybody he sees a threat to the organization. What if we assume the boss is the same if not worse? Killing they're own daugther might be an afterthought to them.
-The boss's favourite is Vermouth. As of now it would seem pretty difficult to connect the two so that is a factor against my theory.
-Then there's the unknown information such as how their name relates to the orgainization's name and also how it relates to that seven crow business.
I've also been thinking of possible scenarios for havng Haibara's father/mother as the boss. For example let's say it's her father Atsushi and he killed his wife because she wanted to free Haibara and her sister from the organization, and pretended to kill himself off and became the boss of the organization (Maybe he wasn't the first boss!). Also I thought maybe he could die in the end too, and maybe as he's dieing finally says something decent to Haibara as his final words like "sorry". Although only saying sorry might be a bit lame of an ending .
Lemme know what you guys think, and also I just made this account so... Nice to meet you guys!
