Sooo many things going on, where to start.
Theories confirmed or pretty close to confirmation:
Bernard is the Host version of Arnold.
Arnold is dead, killed by Dolores.
Arnold is kind of a ghost in the machine, in that his code is all over the place and he lives in the memories of the original hosts, which they see and which they experience with the same force and clarity as they do present events.
William and Dolores in their adventures are definitely in the past. Confirmed when Logan cuts open Dolores and we see the old machine-like robotic host workings of the early days of the park.
William seems to be en route to becoming the Man in Black given the way he butchers his former captors.
So where does that leave us? Here are my final episode predictions.
Dolores, I am guessing, goes back to Tester Town, where they train the hosts There she shoots any that get in her way, and goes through the church, where she sees the hosts going crazy and arguing with the voices in their heads (their Bicameral minds). She goes under the church to the work shop and after some sort of discussion, kills Arnold.
Above ground in the present the Man in Black reveals to Dolores he is William and the past and the present sync up. End of Dolores/Man in Black story for season One (their might be some additional stuff, not sure)
In the past William goes looking for Dolores in a park that is rapidly descending into chaos, he might find her. Either way Ford pulls some final switch that shuts everything down and ends outbreak of sentience. We’ll probably see a whole lot of crazy going on then as well, William might end up killing Logan and making it look like an accident. William goes to marry into the Delos family and his star will rise.
Meanwhile, in the present, Maeve and Hector get to C&C and start building their army and trying to gain control of the complex. This could be the big cliff hanger for the season.
Maeve seems to not only be able to sense other hosts, she seems to be able to look at the code inside of them. How hard would it be for her to take the Arnold parts of the code and inject it into the newer hosts, bringing them closer to wakefulness as well?
Ford has back doors into all the hosts. Does he have additional secret controls as well, he seems a little too thorough to just place all his trust in only one master shutdown tool.