4. The Boss - Metal Gear Solid 3: Snake Eater
It didn't feel right to have a list of bad guys you should be ashamed to kill and not include a Metal Gear entry. While a fair few people have sobbed over a few iconic deaths in the series the one that makes this list is The Boss from Snake Eater. Introduced as the primary antagonist of the game, The Boss's betrayal of America and defection to the Soviet Union become clearer as the game progresses, culminating in the reveal that her defection was planned, as was her death at the hands of Snake. Being the mentor of Snake, it is clear that there would be a lot of emotional and heartbreaking moments in the game which leads to the final boss fight, and as the details of the defection are revealed, but what really puts her on this list is the ending. After everything is revealed before your eyes you fight it out with the one person who taught you everything you know. The music plays as the battle comes to an end. Then, after all is said and done you hold the pistol up to her head as if it were a cut scene, until you find out it isn't. This battle isn't over until you pull the trigger and finish her yourself, making it one of the most heart wrenching moments in the Metal Gear franchise. After her death Snake is given the code name Big Boss to show his surpassing of her, which kinda feels like a dick move. The man just went against his own emotions to kill his mentor in a planned strike and you're congratulating him. At the very least, a different code name would have been nice.