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. Many played the rest of the game in a depression that they just killed Snake's love interest.
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 without the "continue" button as Ocelot pointedly states beforehand...
At least one player accidentally walked into this his first playthrough, neglecting to save beforehand, and then hitting select in order to do that, forgetting that that's how you submit.
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 to shed. But we all knew that he also did inside.
The remake manages to make it just a little worse. In the original game, it was just Snake and Otacon keeping Wolf company in her final moments. In the remake, half a dozen wolf-dogs, the closest thing Wolf has to family, come and surround her, keeping her company. When Snake fires the finishing shot, they all give mournful howls. And the icing on the cake? If you read The Last Days of FOXHOUND, it's likely that one of those wolves was Berthold.
You know how well done Sniper Wolf's death is? In that scene, Otacon yells "What am I fighting for?"note a line better known for being also used verbatim in Mega Man X4 in a particularly Narmy way without sounding cheesy.
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.
Right before said scene, Snake sees Fox trapped on the wall by Metal Gear and he cries out Fox's name. But the way Snake cries out his name, it sounds like he can barely keep himself together and is holding back tears at this point, realizing his best friend is about to be killed for real.
Gray Fox: Snake... We're not tools of the government or anyone else. Fighting was the only thing... The only thing I was good at... But at least I always fought for what I believed in. Snake... Farewell.
The final scene of the game, where Snake tells Naomi that Frank wanted Snake to tell her that he wanted her to move on, and that he'd always love her, while refraining from telling her that Frank killed her parents, knowing full well what the knowledge would do to her.
Naomi was so obsessed with avenging her brother, and yet she ends up regretting injecting Snake with FOXDIE. Snake doesn't even deny she has a right to revenge, but he puts the mission first and says he has to destroy Metal Gear REX before he goes.
In the bad ending, which happens if you give up during the torture, Snake finds out that Meryl had died. In sheer badassery and manliness, he punches the floor and breaks down over the fact that he can't protect anyone, and wherever he goes, people around him die. He failed, and his broken voice really makes it sound like he's crying.
Snake: Forgive me... Damn! I gave in to my fear! I gave in to my pain! I sold your life to save my own... I'm a loser! I'm not the hero you thought I was! I'm nothing! Meryl... I'm sorry... Forgive me.
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.
Psycho Mantis' final moments, a truly poignant moment showing him to be more than just some kind of monster where he tells Snake his origin and dies with some semblance of happiness.
Psycho Mantis: This is the first time I've ever used my power to help someone. It's strange... it feels... kind of... nice...
While many of the '"Snake! SNAAAAKE!"' screams you get from the cast when you die border on narm and have since almost become a joke unto themselves, Mei Ling's screams (easily heard if you die fighting Liquid atop Rex) are gut-wrenching to say the least. They're the kind of helpless, anguished and heartbroken howls you'd expect from a woman who just watched her husband or child get shot dead.
During Snake's Heroic BSoD over Meryl getting shot and captured, Master Miller tells him during a Codec call, "Stop attacking yourself for things that happened in the past! That road leads to madness. Believe me." Given that Miller is really Liquid, it sounds as though Liquid is perfectly aware that what he's doing is wrong, and is voluntarily looking for someone else to blame.
The song "The Best is Yet to Come", which plays during the most poignant moments in the game. Especially if you know Gaelic (or found an English translation of the lyrics).
Please tell me we're not alone
In this world fighting the wind.
Life can be simple if you can only see
The best is yet to come.
If you somehow kill Meryl during the Mantis boss fight, the way Snake screams out her name makes it sound like he realized what he just did and all he can do is collapse by her body in pure anguish. Campbell calls Snake asking what happened and Snake can only utter Meryl's name. The same scene plays out if you allow Meryl to blow her brains out from Mantis's mind control.
, 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 to shed. But we all knew that he also did inside.