i don't think it's Agasa since Haibara is living with him. if he's the boss, he can kill Haibara right away without asking the BO's members wasting time searching for Shiho.
I'll feel great if in the final ep, three Shinichi appears to confused the BO :mrgreen:
1) Conan took the antidote
2) Heiji helped him and disguised as Shinichi
3) Kaito also helped him and disguised as Shinichi
just my imagination~