Isn't that what the show eventually suggested towards the end? That the government was up to such horrible things that if the people ever found out, they'd revolt? That they came up with the alien thing as a smoke screen to cover up the real truths about experimenting on humans genetically and in other ways?

This is good news. I loved that show and still watch it on Neflix sometimes. Lots of shows have tried to copy it since then, but it's still the best of its kind. I hope it does so well that they decide to bring it back for longer. Let's hope it works out better than the attempted comeback of Knight Rider :)