Ok, question about Plague Rat’s various cards that tell you search the villain deck for other cards. I.e. Noxious Bite;
“Search the villain Deck for a copy of the card Infection. Put it into play. Shuffle the villain deck.”
At a point in the game this came out, all instances of Infection we’re either in play already or in the villain trash. So, do I get to laugh in the villain’s face, or does this trigger a reshuffle of the villain trash into the villain deck so he can start infecting people again?
You get to laugh in the villain's face. It doesn't mention the trash so it doesn't apply to the trash. You searched the deck and found nothing. Sucks to be a giant abomination of science, I guess.
However, you do have to shuffle the villain deck, even if you knew there weren't any Infections so didn't bother to even look. This could screw things up for you if you've looked at or moved around cards with things like Wraith's Infrared Eyepiece or some other power.
The same goes for the Chairman, if the Operative is still active and you know all five Underbosses are already accounted for (ie, not in the deck because they're in play/in the trash/under Savage Mana, etc).