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Tear Jerker: Myst
Saavedro's plight in Myst III: Exile. Trapped between a few Ages, convinced that his people are all dead.
The line that hit this troper the hardest?
"I couldn't do it. Atrus, I'm not you."
That line really stuck with this troper, too. As well as,
"They took everything I had! My wife! My two baby girls!"
Pick an ending. Most of them are tear jerkers, be they sad or happy. I found the one where you leave Saavedro trapped forever to be particularly sad. Also the messages Saavedro leaves, especially as you enter each answer into the thing with the book to Narayan. The way he left the last message untouched, so it was Atrus, proud of his boys getting so far on their own... *sniffle*
One easter egg gives you a glimpse of Saavedro with a stuffed animal on his shoulder. You get the distinct impression it's a Companion Cube to stave off his crushing loneliness.
His mural of his wife is left incomplete. Saavedro honestly can't remember anymore what her eyes were like.
This troper was completely crushed after she finished rescuing Yeesha from Dream... and promptly realized that, in so doing, she had just acted as her favorite character's executioner (Sirrus). And then came the above. The fact that she had gone into the game expecting that it would be like the previous three (i.e., Everybody Lives) just made it worse. SO MUCH WORSE.
It's sad if you've read the journals from the original game, and the novel "The Book of Atrus" which depict Sirrus and Achenar as very innocent seeming children. Compare those to what they turned into and ultimately ended up happening to them. That is very tragic.
Say what you will about End of Ages, but the intro is quite affecting, and it leaves you with an uneasy mix of nostalgia and a sinking feeling before the game has even begun. Atrus just sounds so tired. Rand Miller may not have liked playing the character, but he did it well.
There's also the bad endings. This game is one of the most deliberately depressing examples of Nostalgia Level.
Atrus' situation in the very first game. Having to essentially kill both your sons because they grew up to be so evil? It's a wonder he recovers as well as he does.
Watching the mother bird from Exile struggle inside the carnivorous plant's maw, crying piteously for help.