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Shield always seems to be wandering all over the place, like they don't know which direction the story is going episode to episode. That said, I get the feeling that they'll eventually go back in time and fix the bad!future and we'll get to see all the people from this current bad!future living happy lives... only for some other danger to threaten good!future and the good!future characters coming back to 201x to get Shield to help, and the Shield folks will be all "hey, it's you" and the good!future characters will be all "who are you?"
I feel like they've understated the idea that the monolith has taken them to a future in an alternate universe (and not their own), where Quake is Destroyer of Worlds. It does get a little difficult to follow if an episode is missed, but luckily I've watched every single one this season.