So, I'm like a lot of people here. My mind hurts thinking about where/when everything is at the end of season 2. This was an absolute mind-**** of a season.
My thought on the MiB seen at the end:
It's a super "in-the-future" type of consciousness. I think a host-descendant in an "Emily body" is working on recreating genuine humanity. William is a test subject, but not a host. (Because he is super evil? Because he killed her, she wants to make him suffer?) - So, I think robots/hosts have taken over the planet.
Season 1 and 2 proved humanity can be tested. Humans are just more code. (Maybe William is a host at that point, and his consciousness is there, and his daughter wants him to suffer?) I mean, when Emily takes William from Aketcha earlier, she says that he will suffer more with her. Maybe this is what she meant? And being taken by her, instead of staying with Akecheta, he continues farther on his loop where he shoots and kills Emily... presumably over and over and over again. Thus, William is being tested for fidelity IMO.
But, what do I know? Just a guess.
It was cool though.