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Tear Jerker: The Legend of Zelda: Majora's Mask
When you discover that the Deku tree with the horrified expression you come across at the start of the game is in fact the Deku Butler's son. Part Nightmare Fuel, part Tear Jerker.
It should be noted that the Deku Butler's son is who you transform into when you use the Deku mask, most likely. You transform into Mikau and Darmani after they die, so it would make sense because the son is, well— dead. Skull Kid must have had something to do with it.
Epileptic Trees say that Skull Kid killed the Deku Butler's son specifically to fuel the curse he puts on you.
The Deku Butler crying in front of the tree during the credits counts as well. He's one of the few to not get his happy ending...
Then, of course, there's Darmani and Mikau's deaths, which become worse when you realize that you're effectively impersonating them in their societies. Which, if one thinks about it, just further exemplifies Link's heroism. Link does what he does, not out of a desire for recognition, or for glory, but simply because it's the right thing to do. And if doing the right thing means having to make the people think their hero is still alive so as to rekindle the hope within them, or letting them attribute all your hard work to another warrior, then so be it.
The cutscene you get after you heal Darmani's ghost will make even the most hardened Zelda fan feel funny. The cutscene starts with Darmani's ghost simply floating alone in darkness when suddenly the room lights up, showing all of his Goron friends and family cheering him on with the Song of Healing playing in the background. It would go under heartwarming, but Darmani is dead and unable to help his fellow Gorons at all. The scene ends with him resigning himself to Link in mask form, knowing full well he failed his people.
That whole sequence is the most soul-wrenching thing in Zelda history outside of the ending of Link's Awakening. His sheer despair at being helpless to save his people is so thick you'd think you could cut with a knife, and then you find that what killed him is something that's so easy to solve for you, which makes it seem ten times crueler. And then you go into the Goron town and have everyone so overjoyed to see "Darmani" back, including the one Darmani was like a father to, and knowing that they're wrong and will have to be crushed all over again...
Playing the Song Of Healing to Mikau: He floats in darkness when Lulu and his bandmates appear, and he picks up his guitar for a final jam.
Mikau and Lulu's story is heartbreaking. She and his other friends don't even know that he died, and Lulu had just given birth... those children will never know their father.
Which is worse: helping Anju and Kafei reunite barely an (in-game) hour before the moon hits, or, if you screwed up, talking to Kafei after he returns to an empty room?
The dialogue between Anju and Kafei makes it all the worse. "Please take refuge. We are fine here. We shall greet the morning... together."
If you fail to stop the conveyor belt before the Sun's Mask gets to the end (which will really only happen if you choose to let it, seeing as it's a rather slow conveyor and the rooms are easy enough), you and Kafei are trapped inside Sakon's hideout. You can warp out, but Kafei is stuck there. And he won't talk. He just stands there with that blank expression.
Then there is the part of the game where you meet a little girl who seems to live alone in a house in the middle of Ikana Valley (a desolate wasteland of death and ghosts). Upon investigating her house you come across a closet and open it... and find a horribly disfigured half mummy/half human... thing. Turns out that that's her father! Simply imagining all the suffering the girl has had to go through without a father and all alone is a large tearjerker.
The good news though is that he is healed and that they become a family again which quite frankly is one of the most touching moments in the game which considering the game, is really saying something.
And then, as she cries and her father wonders what happened, she just says: "You had a bad dream. You just were having a little nightmare". That's right, the little helpless girl who has witnessed her beloved father turn into a mummy is reassuring him to make sure he never knows the horror they went through.
The story of the swordsman. When asked about the moon, he claims that the moon will most certainly not fall and if it does, then he'll just karate-chop it in half with his awesome skills. Naturally you'll want to see him in action, but when the third night finally arrives, he's nowhere to be found. If you explore the dojo, you'll find a plank of wood in the back. Break through that and you'll find a small, dark room... and there he is, absolutely quaking with fear in the fetal postion shouting, "I don't want to die!" There are simply no words for this.
Try waiting until the final hours of the third day, then talk to as many people as you can, sadness peaks for characters like the mail man who is so bound by duty that he feels unable to leave.
The gate guards also deserve mention. Usually, when you try to leave town as normal Link, they stop you because they can't allow a child to go out on his own, but then let you go after they see you have a sword. In the third day, however, they stop you because they are desperate to know if there's an official evacuation order and then they tell you how much it crushes them to still see kids playing around town.
Right as the moon is about to crash, some guards will have their hands over their hearts.
If you talk to Romani and Cremia after they leave the barn to go to the house, they both say "see you tomorrow", but in different ways. Romani says it as she would if it were any other day seeing as she doesn't know that there may not be a tomorrow. Cremia pauses for a moment, as if debating whether or not to say it when she knows it may not be true.
If you walk in on them in the barn beforehand, they have an equally-wrenching conversation. Romani excitedly explains to Link that she's being given her own Romani Mask and that Cremia is allowing her to drink Chateau Romani for the first time ever that night. Chateau Romani is something only given to adults and the obvious implication is that Cremia knows that this is the end for all of them and Romani won't have another chance. Cremia caps it off with an absolutely heartbreaking request:
Cremia: Romani... sleep with me in my bed tonight, OK?
A really depressing interpretation is that she's trying to get her sister drunk so that she'll fall asleep before the end comes, so that her senses will be dulled so that it wont be painful or that she wont realize what's happening, etc etc
Fail at the part where you need to defend the barn from aliens. Romani is taken along with the cows, her fate unknown. Come back the next morning and enter the barn. Cremia is sitting there, sobbing to herself, not even reacting when you talk to her. She sits there for nearly a whole day. Come back the next day, and Romani will be back outside, staring at you with no emotion at all. The game lacks voiceacting, but you can just imagine her speaking totally monotone.
Dawn of a New Day. Particularly the part with the Skull Kid. He looks up at the giants, who, having finished their role of stopping the moon, are starting to return home. The Skull Kid, who was only corrupted due to his IMMENSE loneliness, is shocked that the giants remember him as their old friend. He realizes that all the trouble he caused was for nothing, and he stands there, shaking and crying, as the Giants go home.
It's even better if you've listened to the stories from Anju's grandmother and realize how very, very old the Skull Kid must actually be, and the fact that he spent most of that time thinking that his friends no longer cared about or remembered him.
The (chicken herding) dude with the mohawk. His backstory is nonspecific, but suggests that he has lead an incredibly lonely, sad life. And then he just accomplishes one thing. And then he's ok with dying. He doesn't ask for his wasted life back. He just wants to do one thing and then die.
On the second day, Anju goes to the Clock Town laundry pool in hopes of seeing Kafei. If you talk to her, Anju breaks down crying and admits that she's afraid to talk to him because she'd have to ask why he left, and thinks it's because he doesn't love her anymore. Damn, just... damn.
If you overheard a conversation Anju has with her mother following the night of the second day, her insecurities of Kafei's love to her stemmed from her mom being 100% convinced he left her at the altar for her best friend, Cremia, because according to Mom she's prettier and Kafei will gain much more from the business Cremia has than the Inn Anju tried to run.
To add to it, the family's already been through a similar incident, as the above conversation and another at the ranch reveal; Anju's father left at some point, and her mother had spent some time hoping he'd return one day, to no avail. She's come to believe it's happening all over again to her daughter. Sure, she turns out to be wrong about Kafei and Cremia. Still, given that she's just trying to keep Anju from going through the same heartbreak she did, especially at a time when their own survival is in danger, it becomes a little more understandable why she'd say those things...even though said backstory gives Anju even more reason to feel that Kafei might have abandoned her, possibly eloping a close friend of hers.
The meeting that decides the fate of Clock Town; nobody's the bad guy, it's a room full of people who can't or won't understand the magnitude of what's happening. Of particular note is the guard commander strenuously arguing in favour of a full evacuation inside the room, then instantly snapping "the mayor's orders are absolute!" when questioned as if he's trying to remind himself of that. The fact that they're debating having a carnival everyone ought to be happy and excited about only makes it worse.
The Ikana soldiers. There's something terribly sad about soldiers who felt such loyalty to their captain that they won't abandon their posts even in death.
You can tell certain soldiers that their jobs are finally over, they salute you one last time and then disintegrate. They could've finally rested whenever they wanted to, but were/are that determined. Deep stuff.
The Skull Keeta himself - the scene right before you get his mask...
"Captain, sir! May I take leave, sir?"
It's possible to help everyone with their problems and still finish the game... with one exception. Do you want to stop Sakon from mugging the old woman? That means Anju and Kafei will never be reunited. Want to help the young couple get married? That means you're allowing a nice old lady to get robbed. In terms of gameplay the choice is obvious, but you'll probably have to wrestle with the morality of allowing a local business to suffer for someone's relationship (and vice versa).
On the bright side, the lady seems to shrug this off and her son seems more concerned for his mom's safety than the fact that their stock was taken. Plus, the bomb shop man says, "next time, I'll go", meaning that they'll get another chance at some point. Failing to reunite Kafei and Anju, on the other hand, is something with more dire and permanent consequences.
Gorman, of all people, ends up getting one of these with your help. With the carnival canceled, Gorman doesn't know what to do anymore, seeing as their huge gig got blown at the same time. Unless you intervene, the guy will spend two straight nights being drunk and miserable at the local milk bar, with his troupe none the wiser. Said intervention being to play the song "Ballad of the Wind Fish" in the bar, this song being the catalyst of Gorman getting into show business in the first place. The effect on him is... touching, considering his overall unpleasant demeanor throughout the game. After deciding to come down with the facts to his troupe, he hands you a mask that is a literal tear jerker to all observers. Especially to his even more unpleasant brothers. A short, yet very emotional sidequest.
Also, if you do it on the first day, he won't go back to the bar the second day, instead opting to stay in the inn and playing cards with the juggling brothers. Nothing big, but still leaves you with the feeling that he's becoming nicer.
Showing the mask to the Gorman brothers is a minor one as well. Seeing their brother's face, they weep for their wasted lives.
Majora's Mask is such a Tear Jerker-fueled game that even the commercials are bawl-worthy. Makes you kinda sad when you consider that the commercials for Majora's Mask all featured a kid saving the world by beating the game in three days...
The Moon's Tear, when you think about it. The moon is crying. Even it doesn't want to go through with this. ThisBrawl in the Family strip manages to sum it up pretty well.
The game of hide-and-seek with those mask-children on the moon. There was just something about the way the boy wearing Majora's Mask sat under the tree with all this calm, serene scenery surrounding him, all alone, lamenting how the other kids were gone... then asking if you wanted to play with him.
The questions of the Lunar Children. ("I wonder... If you do the right thing... Does it really make... everybody... happy?" "Your friends... What kind of... people are they? I wonder... Do these people... think of you... as a friend?" etc.) They aren't the bad guys; they're just misled and ignorant. And very lonely.
Yes, the Goron Elder's Son has Most Annoying Sound going for him, but he's just a little kid missing his father and, on top of that, it's doubtful that anybody has managed to explain "Darmie's" death to him, as young as he is. He's lonely and probably scared; no matter how well he knows the other Gorons, sometimes there's no substitute for a parent. This will definitely hit some people harder than others.
And then when you play the lullaby for him and get a scene of his father cradling him. Made worse when you realize that his father is very elderly and feeble and probably doesn't have much time left.
The whole premise of the game is that Link's on a journey to find the one friend who's closest to his heart because she left him at the end of Ocarina of Time. He never finds her.