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Tear Jerker: Metal Gear Solid
Those who entered the game with little idea that there was a bad scenario, when you fail to restrain yourself from the torture, you realize you just killed Meryl. I played the rest of the game in a depression that I just killed Snake's love interest. Perhaps the most immersive moment in any game I played.
To make things worse, try playing the game and attempting to resist the torture, but having to surrender because you haven't saved for half of the game, and death there brings instant game over.
It gets sadder. You know how Campbell tells Meryl for most of the game that she's his niece? If you get the bad ending, he actually reveals that she's his daughter.
There have been many sad moments in video games before and after. And sometimes there have been vilains that got a bit of sympathy. But how often do you stay with an enemy you just shot, as she bleeds to death in the snow, in a dark and cold winter night. Well, you do for Sniper Wolf, and it's one of the saddest moments in the entire game. That day, Snake was the only one who was not crying, and only because he had no tears left. But we all knew that he also did inside.
The full line perfectly sums up Otacon's character at that point. Having just witnessed someone he loved die in front of him, by the hand of a man he's growing to respect and look up to, all he wants to know is how it came to that.
Otacon: (Snake starts walking away from Sniper Wolf's body) Snake! What was she fighting for? What am I fighting for? What are you fighting for?!
Snake: (turns to face Otacon) If we make it through this, I'll tell you!
His death is made even more sad by Snake finding himself unable to put him out of his misery when he's being held against the wall by Metal Gear: "It's no good! I can't do it!" The line is even better in the original PSX version. The way Snake says it is out of sheer exasperation and defeat. He wants to end it, but can't bring himself to fire and kill his friend too.
The final scene of the game, where Snake tells Naomi that her brother told her to move on and doesn't tell her that Frank killed her parents.
The bad ending has Snake, in sheer badassery and manliness breaking down in tears and punching the floor over the fact that he can't protect anyone, and wherever he goes, people around him die.
And Otacon consoles him by saying that he and Sniper Wolf will meet up again in Heaven, so Dave and Meryl will, too. Such simple faith, after all the crap that Hal's been through. Such simple faith that people do go on to a better place, and that Snake is good enough to have a happily ever after.