Bernard is the one who makes it look like Dolores is dead by shooting her and flooding the Forge, but really he hides her inside robo-Hale and scrambles his own memories so that Strand and his security can't access them. Dolores-as-Hale smuggles him out of the park and rebuilds him but she says that she and Bernard will not be allies out in the real world.
And while it was a wonderful surprise to see Anthony Hopkins drop by for season two, since it turns out his season two appearance was all in Bernard's head, it seems like Ford's role may be over. Or not. You never know with Westworld.