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Tear Jerker: Lufia
The ending to Lufia and the Fortress of Doom is particularly poignant, though it ends on a hopeful note.
The ending of Lufia II is perhaps even sadder, especially since if you played the first game, you know what's coming.
Try and imagine what the ending of Lufia II is like if you've never even heard of the first game.
Lufia 1 had you playing out the end of that story already. So if you've already played the first one, the second one is only making you go through it all over again.
Lufia & The Fortress of Doom has Arugo and Hero's conversation after The Reveal, wherein Arugo asks how Hero plans to deal with Lufia's very existence enabling the Sinstrals to endlessly reincarnate. Arugo starts to suspect Hero is actually willing to kill her to break the cycle — and to make matters worse, Lufia overhears this part.
The ending has Lufia live at the cost of her memories and magic.
Guy's death in Lufia 1.
The ending to Lufia: Curse of the Sinistrals is a tearjerker for a different reason. Being a re-imagining of Lufia II: Rise of the Sinistrals, the game finally has a happy ending if you beat the game on New Game+, which means that after 15 years since the game's original release, Maxim and Selan finally get to go home and raise their son instead of dying on Doom Island.
Lufia II after Maxim and Selan die on the Fortress of Doom, the ending shows that everyone thinks that they're going to make it out alive and that they'll see them tomorrow at the big party Guy is going to be hosting. Also, seeing their child Jeros, cry out for his mama during the same sequence is heartwrenching enough to elict a few tears for the now orphaned child.
Seeing Tia leave without even saying goodbye (except to Dekar), never to be seen again, too sad to see Maxim, and can't even bring herself to cry is sort of a Tear Jerker. Or maybe a Tia Jerker.
Lufia: the Legend Returns has the ending, where Seena dies, and is brought back to life a year later due to the power of her desire to see Wain again. But she must stay with him forever because of that desire bringing her back, and if he ever lets her go, she'll die. It doesn't help that Seena and Wain's powers are gone, and Seena experienced death before being brought back.