Here goes:
1. Ran is the leader of the Black Org, who took some form of the ahoutoxin and shrank into a ... lets say three-year-old. She was then adopted by Mori Kogoro and Eri, which happened because Eri is really a BO member. She has been running the whole thing from behind the scenes, using Kudo Yusaku as her secon-in-command. She knows that Shinichi is Conan, but doesn't really care since she really does like him, even though she should really be like, forty. Vermouth is the favorite because she is Ran's adopted little sister.
2. Eisuke is the leader of the BO. (see above. the only diffrence is that now that he knows Conan=Shinichi, he wants to get the other guy out of the way so he can marry Ran.)
That's my crack.
My real theory that I think could work but sounds like a crack theory is this:
Eri is a BO member, while Kogoro is a member of Shinichi's mom's secret anti-BO group, the "seven knights", which included Kuroba Touchi.
Korogo and Eri seperated because he realised that she's a BO member, while she doesn't realiase he knows.
Mori Korogo has also known about Conan=Shinichi for quite some time now, and is just biding his time until the perfect moment.
And I do very very much like this one:
TheBlind wrote:The Boss of the BO is actually Hattori Heiji. ... When it all said and done, Kudo will be standing there feeling triumphant over Gin's unconscious body with sirens at the distance when he'll hear a friend congratulate him from behind. This conversation will end with Heiji saying "You were the closest thing I had to a best friend Kudo..but Business is Business and don't worry, I'll take care of your girlfriend for you" *Gunshot*
So Haibara's "radar" goes off at odd times, right? And she thinks that it is linked to the Black Org, right?
But all of the times it's gone off, there have been FBI (or suspected FBI) members there...
So, it's an FBI radar.