Key points -
Maeve's privileges go all the way to the top (she could control Bernard). Given what happens between Ford and Clementine at the end, this may prove significant.
When Logan eviscerates Dolores to 'prove' to William she's not real, exposing her '1st generation' innards, Dolores reveals inner knowledge - "There is beauty in this world, Arnold built it that way". She's more clued in to her reality than she lets on.
After fleeing, Dolores stands, checks herself and is now not wounded - the whole Will & Logan saga is a memory, not the present.
Charlotte Hale confirms MiB is a senior board member of Delos, he says he doesn't care about whether Ford gets the boot. She also says the MiB's investment kept Ford in business "all those years ago".
We see Teddy have a flashback - and just as Dolores did previously, he sees himself as the culprit in the massacre of the original town. Did it repeat itself with different hosts, or was the massacre orchestrated by a handful of the 'sentient' ones?
Elsie's behaviour tablet has been detected - when the already suspicious security guy goes to check, his communication device doesn't get a signal (as Ford did with Teresa's) and the warpainted hosts that Maeve recalled scalping her once, do not respond to his commands..
Logan awakes in the camp the night after the Dolores incident - and everyone around him has been slaughtered.. by William, who is clearly exhibiting the first signs of being the MiB. He tells Logan they are going to find Dolores. Or else.
The buried church is standing in Dolores 'current' timeline (it's not necessarily the actual 'present' timeline, as the MiB in conversation with Wyatt's gang says it's buried) It's the site of the original underground Westworld facility - the confessional booth is the elevator access!
Dolores explores the area, flashing between multiple timelines (all when the church was standing) as indicated by the clothing she wears.
Young Ford walks past, looking for Arnold...
We witness 'Bernard' being 'born' and schooled in the correct mannerisms to mimic who he's a replica of. Who we suspected all along. We see Dolores address him by that name.
We see the famous photo with the real Arnold visible.
We see Dolores in one of those old secret interviews with Arnold - and the point of the inner voice ("remember") becomes clearer:
"You can't help me... because you're dead... because I killed you"
When Dolores exits the confessional elevator again, the Church is empty - and the MiB is at the door. Is this the recent past? Was the Church rebuilt and access to the facility below restored? It was buried in Will & Logans time, and the MiB in the presumed 'present' says it's buried. Maybe he just never went back to see....?
Ford turns the tables on Bernard and reveals he had the upper hand all along. His references to what can happen to the inferior species may be prophetic. He departs leaving us unsure if the gunshot found it's mark, or even if it did, whether that's really the end...