* The ending of ''{{Terranigma}}''. Period.
* The goat scene in Eklemata. And if you come back at a later chapter, [[FromBadToWorse well]][[DownerEnding ...]]
* The game is very good at this, despite having a mediocre translation. There's also [[spoiler:Elle's HeroicSacrifice]] and [[spoiler:the death of Royd and Fyda]].
* During the PlayableEpilogue, the kid looking at the pond: [[spoiler: at the beginning, before [[NiceJobBreakingItHero opening the Pandora Box]], the kid at the pond says the fortuneteller told him the image on the pond was the future, explaining to him why he was seeing so many high glass towers. Then, in the epilogue, he just says that [[QuieterThanSilence he can't see anything on it anymore]]...]]
** In the same part, after hearing throughout the story the same line about how "the unnecessary people will die, and all others will live forever", the shopkeep simply stating that "there isn't a single person who is unnecessary" is just...
* Elle breaking down and crying at the beginning of the game because she fears that she would not see Ark again. [[spoiler:She's completely ''right''.]]
* The moment when Ark learns he [[spoiler:couldn't talk to animals anymore]], when [[spoiler: Leim rescues you]] and when you realize, after basically creating this whole world and [[spoiler:developing the towns (and buying Ark an apartment), you have to leave it.]]
* [[StarCrossedLovers Nana and Servas]]'s [[IWillWaitForYou story]]: You first meet Servas at the Great Lakes, [[InsurmountableWaistHeightFence blocking your way into the cave]]. He insists he cannot leave his spot because he's waiting for his girlfriend, Nana, to arrive from Liotto so they can get married. A bit later in the game, you find Nana... transformed into a mermaid, [[OurMermaidsAreDifferent or the spirit of a maiden who died at the sea]]. Turns out the ship in which she was travelling wrecked, and she drowned. She asks you to give Servas her engagement ring. When you show him the ring, he says he understands and [[DeadAllAlong vanishes into thin air]].
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