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Wasn't there already a story line in the original series where Fox became convinced that all of his alien theories were b.s. and that he was being misled all along? It's been so long since I've watched those old mytharc episodes that I can't remember.
I wish they had just kept the single alien invasion/secret cabal of collaborators story line. The black oil, alien rebels, multiple explanations for Samantha, a second set of conspirators and the other stuff just made it way too convoluted.
Edit: I think "Gethsemane" may have been the crisis of faith episode I mentioned above.
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