Well I was thinking If the character that is the boss has been shown or mentioned in the series a few times and once that person is reviled haibara will be shocked. So we can narrow down the characters to six people. Haibaras family (Father, Mother, Sister and grandfather), Shuichi Akai and Agasa. It cannot possibly be Agasa because the boss wants Haibara dead and Agasa is like her guardian which he could've killed her long ago. It can't be Akai because he is deeply in love with her sister and has saved her in the previous BO action on the train. (Subaru is Akai). It can't be her sister because she has died by the hands of the org. Now It can't be her father or mother even if there is no proof of them dead but they are just to young to be the boss. The BO has been for 50 years now and her father should be around 54 years old because his best friend was 54 years old but then again his age is unsure. So I have no proof of them being the boss. On all these facts I say that boss is haibaras grandfather. I do not have any clue of him being dead or alive. Or him being mentioned in the series. But if you go now and check the page on this site about Atsushi Minayo (Haibaras father) and scroll down a bit to his relatives. It does say that he has a father but it's unnamed. Now his age is enough to be the boss because he should be about 60-70 years old. And if your thinking that he should be dead due of old age then no, why you ask? Well because vermouth is the boss's favorite subordinate and she has never changed her appearance even that she is old and she has been able to fake her death as Vinyard and look young always. With some kind of drug both her and the boss can stay young for a while. So this could be a reason why vermouth is the boss's favorite subordinate. And mostly bosses of secret organizations are ruthless and will kill anyone that gets in they're way including they're relatives. So wanting to kill her niece cause she left the org and let out a lot of secrets is not weird at all. So this is my theory on the boss of the black organization. And the organizations name should be The Miyano Org or something related to that name that's why Gosho didn't tell us the org's name because the boss's name will be reviled.
