How did you choose to implement the Theme: Alien Infiltration in your game?
We had aliens as the main bad guys, per say, and the idea was is that the aliens were working together with the government, or just flat out had control of it, and were "improving" humanity by converting them into aliens. In fact there is some cut content I specifically made, that would have went deep into the experience of one of their test subjects.

Did you implement any of the optional Bonus Challenges, and if so, which ones?
We planned to implement all three, however, I do not remember if we got any or all of them, at least within the actual game. We had planned to have a doppelganger scenario, and I wrote some unimplemented (I think?) bloody notes that would have described the horrors of one of the aliens test subjects. Also, The aliens were working with the government to Convert everyone, so that would have covered all three.