The Second Half of The Story:

As far as Bonanno was concerned (in 1963) he was the last Chairman, at the last "Official" and "Unofficial" meetings, which happens to be true. Gambino (of course on the streets) was head of his Family but not "on paper" in Bonanno mind because it was ratified in a "Official" Meeting. (If you remember, one of the reasons Vito Genovese rushed the Appalachian meeting because he wanted his position in the Luciano Family ratified during the meeting.) Angelo Bruno and Joseph Zerilli were assigned to inform Bonanno to Come in for a meeting but Zerilli didn't have a dog in the race and went back to Detroit. Bruno and Sam Decavalcante tried to intervine but The Plumber wasn't on the Commission and Bonanno didn't respect Bruno as a Boss. (Bruno was endorsed by Gambino who in Bonanno's mind wasn't a Official Boss yet.) So Bonanno refused the meeting and went on the lam from his impending legal issues. (I also wanna point out that during these times Bonanno was still seeking and acquiring other business opportunities. He was just "hiding" from enemies or law enforcement agencies.)
Lucchese and Gambino used Stefano Magaddino's Senoirity to usurp Bonanno's "Chairman" status and they conspired with Joe Colombo, Tommy Eboli and Jerry Catena to removed Bonanno. Why??? Over Drugs, Territory and (probably) some Union and Garmet industry racket seizure.

Stefano Magaddino comes into play because he and Joe were cousins. The jealous of his younger cousin gaining more prominence in America and within there Castellamarese Clan was stinging. And the Paolo Violi situation was a legitimate beef but I really believe the fact that Bonanno left Magaddino out of the Heroin business and his expansionist plans was the biggest bone to pick there. For whatever reason, Bonanno never wanted to couple with Don Stefano. Perhaps, he didn't think Magaddino was as astute as he was. This is what also brings Gaspar DiGregorio into the picture.

Gasparino represented a strong group of guys mainly from Longn Island but some from the Brooklyn homebase. But he was the brother in-law of Don Stefano and for that reason (I believe) him and his group was mainly kept out of Bonnano's "drug clique". That's a huge source of cash to kept out of and have to pay exorbate tribute on top. That's a fault on Bonanno's part, but he could trust DiGregorio and Magaddino's association (If you remember in the Sopranos, Tony didn't wanna give Ralph a piece of the casino because New York was partners and he didn't wanna give him access to Johnny Sack.) He would prove to be right. This is the only logical reason I could come up with forthe Family spliting apart. In reality, its always OVER THE MONEY!!!

In the case of Bill Bonanno, whether he was "elected" or "placed" as Consigliere is iffy for more. I see both angles and truely believe, its alittle of both. Thats being said, he didn't belong in that position. Period. As a street guy, he supposedly had an opportunity to whack Gaspar himself and didn't. (That's his words). But end of the day, it was about the drug money not flowing in Long Island. Frank Mari was getting his drugs from Joe Beck DiPalermo on the side. The more street side of the Family in New York who weren't tightly associated to Carmine Galante weren't really apart of the "Clique" which was his associates (in NY & Canada) plus Bonanno's relatives (Bonventre/Magaddino/Labruzzo/Bonanno). That leaves alot of guys on the outs : Gaspar, Sciacca, Smitty D'angelo, Rusty Rastelli, Nick "The Battler " DiStefano, Mike Adamo, Mike Consolo, Nick Alfano, Angelo Caruso. Aand alot more. The Bonanno Family doesn't get the credit it deserves because even it had some earners and and some dangerous guys. Frank Mari for instance was definitely more capable any any capacity than Bill Bonanno.

And by all means based on the rules, they had a right to want another leader. But Bonanno still bolstered a loyal to the end group. (Which to me speaks the loudest.)
The Family fought, Bonanno lost the war and Paul Sciacca was elevated to Boss of not the same organization. He had to whack out a few contenders but that was that. Family issue resolved.

One last thing I have to point out, in the mid-60s Bonanno was allegedly offered the opportunity to run the "Coffee" trade ( code word for heroin) in Haiti directly by its dictator, Papa Doc Duvalier. At some point the island a been occupied (similarly to Cuba although lesser in scale) by La Cosa Nostra particularly the Gambinos. There were abandoned Casino to be rejuvenated and another hub for the Heroin trade being offered to Bonanno at a meeting that Bill had there. This also is an affront to the likes of Gambino. I do believe Gambino had a claim on this territory but the beef isn't legitimate because the opportunity was brought to the Bonannos.

The aftermath:
To me, its obvious that the end game was to remove Bonanno so that the Lucchese and Gambino Families could become the leaders in the Heroin Trade. Think about about it this way, early 70s French Connection case is Carmine Traumanti (Lucchese) going into the mid-70s you have the Cherry Hill Gambinos. Once Carmine Galante returns, you have to wonder why the Gambinos were so close to his hit??? He would've brought back too much of the old ways (The Bonannos in prominence and being leader of drugs).
They got to knock them out of the Garmet Industry (believe it or not they were pretty lucrative at one point). And who benifited? Tommy Lucchese and Ultimately Don Carlo Gambino.

Bonanno mantain an viable business portfolio, still controlling the Mozzarella cheese industry for a decade longer. He was still a high level emisarry within the international drug smuggling (think to his being informed of the Galante hit). He ran a crew of old timers and second generation relatives who were into gun and jewelry smuggling, loansharking and small business infiltration.

The Conclusion:

*The Commission based on the actual rules they established didn't have the authority to remove Joe Bonanno. Based on a Majority though, they removed him. It is what it is. I don't agree with it, It was a Family Matter.

*Bonanno overstepped his boundaries and the size of his empire crumbled under its own weight. I do agree Bonanno was out of line (in totally) but I don't think he committed "Killing Offense's".

*The Bonannos (like every Family) should be able to elect their own boss. No Commission approval needed. If you are the "Rapresentante" you represent a group of people. That group should be strong enough for you to be respected and acknowledged as a "Boss".

*Bill Bonanno had no business being in the Hierarchy. No argument here.

*The Commission that most mob enthusiasts understand is how it operated after 1968. The Original 1931 Commission is misunderstood.

*Tommy "Three Fingers Brown" Lucchese is the real puppeteer. Although Carlo Gambino reaped the ultimate rewards, it was Lucchese who orchestrated this. Lucchese could've been the Boss of Bosses if he lived longer.

*The Bonannos (post 1968) aren't the same organization (or drawing from the same historical lineage). And lost power, prestige and money.