So many little details in Alpha Protocol. As janky as that game was (no could be about it, it was janky), there was so much effort put into details like the order you did missions affecting later choices (Did you do the Hong Kong missions before Russia? Congratulations, you can have one of your contacts from Hong Kong poison the main boss's cocaine!), or a character you meet casually bringing up something you did in a previous mission...
Or my personal favorite, getting one of the characters to let you kill them in a boss fight. See, this guy is a professional through and through, and he'll cut and run rather than fight it out. Unless you are everything he hates, by acting casual every time you talk, sacrificing the chance to disarm a bomb to save the girl (he expected you to do the opposite), and getting enough intel on him to be able to get under his skin by calling out his past failures. Do all that, and he'll risk death just for the chance to kill you.