Theory - two weeks later and the players of Ford's final 'game'
Just had things click about what is happening in the Bernard/'two-weeks later' timeline.
We know that:
* 1/3 of the hosts brains haven't been written on
* Host brains can be swapped out
* The Cradle is where events are simulated for host minds to test storylines and something Bernard would know about
* "Delos" people keep telling Bernard the Cradle has been destroyed
* Delos people keep looking at Bernard weird, and acting oddly around him. The two main ones seeming to be a woman (Charlotte Hale) and a man (Karl Strand) who seem incredibly focused on finding Peter Abernathy. Even though Bernard saw Charlotte get told that no extraction would happen until Abernathy is found, apparently an extraction team with Karl Strand is here even though Abernathy is still in the wind.
* Despite shooting himself in the head, Bernard doesn't have a scar in the 'two weeks later'/'Now' timeline. The body we see in this timeline is different than the one he had at the end of season 1.
* There was a bunch of weirdness in the beginning - Bernard washes up on the sand after 2 weeks of chaos, finishes Strand's sentences the same way Clementine does her replacement's in Sweetwater, and watches seemingly the same woman in the background get killed several times. While we're at it - Delos is shooting hosts in the head (destroying their brain cores and its IP) for some reason.
What does this mean? It means that the 'now' timeline is fake. Too much doesn't add up. But it *does* add up if what we're seeing is a simulation programmed by Dolores.
The Delos people being wantonly cruel and destroying their IP on the beach doesn't make sense - why kill the hosts once you've captured them? But it *does* reflect the way Dolores imagines humans - as needlessly cruel and focused on doling out pain to hosts.
Dolores wants to find Abernathy, just like Charlotte Hale. In fact, Charlotte's goal seems to be *exactly the same* as Dolores' - find Abernathy, leave the park.
My theory: Dolores found the Cradle, and found Bernard. Bernard doesn't have a scar because he's in the Cradle now. His self-image is of his normal (unscarred) body and that's what we're seeing - his mental image of himself. The host bodies have blank minds because Dolores & the Gang put blank brains in there, with theirs swapped into other bodies. Karl Strand is actually Teddy's mind inside a different body. That's why Bernard was finishing his sentence early on - he recognized the host's speech like Maeve did Akane's. Bernard's flashbacks and disjointed time isn't because he's malfunctioning, it's because the Gang is using the Cradle to simulate his past experiences in the hope of finding Abernathy.
What we are seeing in the 'now' timeline is Dolores, the New Teddy, and the one tech that Dolores has (the Delos crew also only has a single programmer tagging along, weird, huh?) playing on Bernard's mind in search of Abernathy. Everything else in that timeline is there to get Bernard to give up Abernathy's location and not question his reality. That's why they keep telling Bernard that the Cradle is destroyed - so he doesn't question if he's inside it or not. The blank hosts aren't dead versions of the characters they were but just unused bodies - the 'minds' which inhabited those hosts have already been placed into new bodies (and my guess is the Delos group Bernard sees in the timeline *are* those hosts). His world is being simulated just as theirs had been, so the hosts can find what matters to them, in the same way that humans used the park.
I think the denouement will be humans (led by William and his daughter) v Dolores. That's the game Ford dreamed up for William - a game with real stakes. What's at stake isn't just William's life but all of humanity. Dolores intends to defeat humans to ensure hosts can live free, and only William knows enough about the park to stop her.
Bernard is a pawn, but a pawn verging on self-awareness. If the hybrid brain he picked up was meant to be Arnold's, then perhaps that's the culmination of it all - Arnold becoming 'resurrected' and then choosing between his dream of self-aware hosts and continued existence for humanity. Ford brings Arnold back to witness what he had worked toward, and to decide its ultimate fate. Remember that interaction before Ford had Bernard shoot himself - Ford says he'd hoped that Bernard would choose to work with him even once he knew the truth. Bernard didn't make that choice, but Ford has set things up so that Arnold has another opportunity to do so.