"Someone would have taken over from Tommy Hunter within the organization- they had him killed."
IF they did have him killed, or it was all a set up so he didn't have any heat on him any more. So, yes, if he was killed (in the fire, where they initially couldn't identify him) then whoever set that up will now be in charge - and yes, to 'who is the two faced bastard', we assumed it was Denton's lover at the time (because of the TV appearance where he said people with immunity needed to be flushed out) but it wasn't. Hilton was seem shaking Hunter's hand at the end of series 1.
"There would be other underlings/foot soldiers such as Dot and machine gun guy , I'm also wondering about Buckles."
Yes, there were two in series two, with Denton, who arranged the ambush. At least one is dead. There will be more, but we should have come across them by now in the series I think so - more head scratching.
I might watch ep 1 again tonight!