This is a show working way to hard to come up with a bad guy. Which is something that Atlantis ran into.
What's wrong with having this as an "exploration" show; yes, they run into bad guys along the way, but the show sets itself up to be a more "mystery" show.. why did the Ancients travel this way (some of them), what was there goal? Did some of them get off along the way? Did they leave clues? Can we find cool civilizations that suddenly need help or just puzzle pieces?
I think we're struggling with the stones to keep involving earth, etc. when the better storyline is to just say "every week is a new, self contained episode basically with the master arch of the show being: what do we find at the end, and how do all these little mysteries add up?"
Bringing in old enemies, etc.. YAWN


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