Anyways, here's my take: In an earlier posted comment I mentioned that the guy in the trenchcoat was Graves, let me explain further.
Graves and the Minutemen have been functioning fine, working with and for the Trust, keeping everything in line. Then Augustus Medici has a brilliant idea to merge all the families into one big happy organization, but the Minutemen technically can't allow that. So Medici has a plan.
Medici and Graves, who were once best friends, talk, and Graves says "no", but what does he say "no" to? Well, we don't know that. We don't even know if Graves even said "no" to anything. So Graves and Medici have their "falling out" and Graves is ordered to be killed by his own Minutemen. They have no clue what's going on. Sheppard pulls Graves out of there in time and Graves goes underground for 6 months (is it 6?).
In this time, Medici proposes his Trust merger, half the Trust buys it, half of them don't. So that half has to be dealt with. Who better to deal with them than The Minutemen? Oh wait they're all presumed dead. That's when Graves resurfaces. He starts reactivating the Minutemen. And if you notice, the first one he tries to "take out" in Megan Deitrich, who is the newest member of the circle of 13. She alerts Medici who gets angry, he kills the dog because he knew Graves would come back.
So Graves does his thing, Medici does his thing. The first person in the inner circle to die is Daniel Peres. We don't know how strong or week Daniel Peres is, but we know that he's neutral in the standpoint thus far. He thinks the merger is a potentially good idea, but he's still a pretty strong warlord himself. So eliminate him, then divide up his assets. Then (in the story entitled A Crash) Graves meets with 3 of the 12 warlords who are all unhappy with Medici. They ask Graves to eliminate the house of Simone, because it's weak, but that's a bad idea, because Mia Simone supports Augustus Medici. So the next Trust member to be killed is Anwar Madrid. He's another neutral player.
So by eliminating the neutral players first, then the rebellious ones, Medici can slowly take control of the Trust, and Graves is doing his dirty work. In issue 60, Graves meets with Medici, and we have no idea what it's about. I guess that will make my theory sound right or wrong.