[spoiler]At this point we have two storylines.
We now know there’s Arnold’s storyline embedded in the park, “the Maze”. This storyline is out Ford’s control. The MiB follows this storyline knowing that it’s not Ford building it, the MiB merely follows the hidden tracks left by Arnold. Because no matter how Ford (literally) buried his partner doings, they are still there, under the dust.
When MiB kills everyone in that village, and the girl suddenly gets out of character to tell MiB about the maze. This scene of the girl snapping into a different “personality” is an effect consciously triggered by MiB. It’s putting this girl under heavy mental distress so that she snaps out her usual programming and awakens “Arnold”. So, MiB savagely killing hosts is essentially the trick he uses to “break” the Ford overwritten personality to awake again Arnold latent code.
And we know that this “Maze” is the will of Arnold to set the hosts free from the control of human beings. Return them their dignity. Dolores killing Arnold symbolizes a “death of the gods”. She acquires responsibility, and that’s why when she returns to Arnold he cannot help her anymore.
Arnold is a god that “gifts” true freedom, so he cannot tell Dolores what she should do. Her actions are her own responsibility now. She cannot follow anymore a superior morality (or script) set by someone else.
And then we have Ford’s mysterious new narrative. Instead of burying Arnold further, he now digs out the set up of the major fuck up that happened 35 years before. Ford is aware now that Arnold’s code is still latent, that there’s this nagging presence that he still wasn’t able to uproot. We know Ford knows that Dolores is off her loop, for the first time since, and we’ve heard Ford speaking to young-Ford-host, killing the dog after hearing Arnold’s voice. So we know Ford knows that Arnold is still out there, and buried in the memories of some old hosts.
I think this time he’s deliberately awakening that latent code so that he might finally able to erase it radically. He gave Arnold/Bernard a last chance of coming to an agreement and working in the same direction. But even as Bernard, Arnold keeps antagonizing Ford’s perspective, so Ford kills him. A second time.[/spoiler]