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Tear Jerker: Final Fantasy II
A lot of characters end up dying during the course of this game, but perhaps the most affecting death is that of Ricard, who spent a sizeable portion of the game in your party, and moreover takes care of his friend's wife and her son, who the player meets earlier in the game, and have to speak to again if the player wants to obtain one of the game's better weapons. It doesn't help that he had the full intent of raising the son to be the last of the Dragoons, and in the ending the two of them leave the Dragoon legacy behind forever.
Then there's the incident with Josef, Nelly's father. Outside his home, you can see a woman wearing pink, who talks about how much she likes him. She seems to be just infatuated and kind of an airhead, until he dies protecting your party from a falling boulder - then she moves in and adopts Nelly, for Josef's sake.
At the end of Soul of Rebirth, when visions of the party's still-living friends and family appear to encourage them and not fall for the Light Emperor's lies; also, there is Nelly calling out "Daddy!" to Josef. Then later, when the dead party watches their loved ones after the final battle, and Nelly says she's going to help out by working at the palace. Such a strong little girl, just like her daddy.
Then there's Deumion's backstory from the PSP remake, all though there are two scenes that really stand out. The first is the Arcane Labrynth level "Hope". Deumion is being taken away to guard the Destroy Tome for all eternity, despite being just a boy. If you make it to his place before the guards, he acknowledges that he will never see any of his friends or family ever again. The only people he meets after that are Firion and co, due to time travel. As Deumion leaves his mother, she cries out and Deumion drops his trinket. The second is if you chose to fight and kill him for the Destroy Tome. After guarding the Destroy Tome for thousands of years, the most powerful mage of a lost society is rendered helpless against Firion. He claims that he has held on to "hope far too long to give in now", but promptly dies trying, and failing, to stop Firion from undoing his life's work.
Exploring the world right after the Cyclone. Before that, all the towns were half-wrecked anyway thanks to the Dreadnought's bombardments, but at that point? The towns are gone. Nearly every place you have visited—Poft, Paloom, even Altair—is just a shell of ruins on the map that you cannot enter, because there is nothing and nobody left.