Success! Your most diabolical adversary has been captured alive! Surely now we can bring him back to base, interrogate him and dismantle his schemes now that his nefarious doings are halted...right? Somehow his interrogation undermines even the staunchest of men sent to break him. Somehow those captured resources of his create a crucial security fault which suddenly compromises your every advantage. Before you can react, your base is in ruins, the MacGuffin is missing, morale is through the floor, and now we have to take him on at a serious disadvantage. We should have seen it coming. Act 2 wasn't even over. I find it exasperating just how ubiquitous this story device has become since The Dark Knight. Off the top of my head The Avengers, Skyfall and now even Black Ops 2 have abused this plot device mercilessly. It's a subtrope of All Your Base Is Belong To Us and Trojan Prisoner, but with a very specific sequence of tropes contributing to it, such as Hannibal Lecture. I think it needs a page of it's own.
Hello, Unknown Troper. You'll need to get known to lend a hand here.