* The ending, when [[spoiler: the Mirror of Twilight begins to crack and Link and Zelda realize that they will never be able to see Midna again.]]
** [[http://www.mediafire.com/?2qmmkbmogxm That has to be the most depressing moment in the entire series, especially for Link]]. Is it any surprise that [[spoiler:fans really, really [[http://wantmidnaback.com/ want her back]]?]]
** The worst part was his reaction to [[spoiler:Midna breaking the mirror]]. ''[[NotSoStoic Damn]]''.
** This is STILL made worse when at the very end, Link leaves his life in Ordon (his friends, his job, and Ilia) behind to embark on what is likely a futile search for another way into the Twilight Realm.
*** Maybe, or maybe he's just taking Rusl's advice to "look on it all with [his] own eyes" while he's not having to rush around from dungeon to dungeon.
* When Midna [[spoiler: is mortally wounded and Link runs with her on his back in wolf form taking her to Zelda as a melancholy piano piece sweeps in.]]
** And when you reach Zelda, does Midna ask Zelda to [[spoiler:help her? No. Despite being mortally wounded and close to death, the reason she wanted you to "hurry to Zelda" was so that she could ask Zelda to help ''Link'', who had been permanently turned into a wolf by Zant. She may as well be on her ''deathbed'', and Midna doesn't say a word about her own condition.]]
*** [[spoiler:She ''is'' on her deathbed. She's a creature of darkness who has just gotten a full blast from a ''spirit of light.'' She fully asks Link if he could manage without her.]]
---> Midna: Link... you can... get there without me... right?
*** And so, Nintendo decided that particular scene was gut-wrenching enough. No, wait, [[spoiler:Zelda performs a HeroicSacrifice to save Midna. And the worst part is? Midna is ''protesting,'' practically ''begging'' Zelda not to do it...''but she does anyway'', with a serene, encouraging look on her face the whole time. And then she's gone.]] [[ManlyTears Dammit...]]
* Queen Rutela. Especially the scene after she gives Link the Zora Armor.
** [[spoiler: "If you see him again, please pass on this message... Tell him he must not grieve his mother's passing. Tell him she wanted him to be brave and live on as the king of our people. And... Tell him his mother...loves him without end. Tell him... Please tell my son when he wakes...]] The [[http://www.youtube.com/watch?v=4jXTWOM6i3c music]] that plays during the scene doesn't help.
** After she fades away, it pans up to reveal the dawn.
*** The scene in the credits, where Prince Ralis is sitting at the edge of the river and the Queen is watching over him. And then Ralis stands up, and looks as if he swore he could've seen something.
* Hyrule Historia confirms that the Hero's Shade, a spirit which teaches Link many of his special techniques, is none other than [[PreviousPlayerCharacterCameo The Hero]] [[VideoGame/TheLegendOfZeldaOcarinaOfTime of Time.]] He deeply regretted not being able to find a suitable pupil in life and has been chained to the earth all this time, waiting for someone to pass his skills onto.
** His entire attitude about the matter is heartbreaking: this is the Link that saved both Hyrule ''and'' Termina, who later grew up and had a family of his own, and after all of his accomplishments and sacrificesm, in the end he looks on himself as a failure because he wasn't able to do ''even more'' to help.
* The look of absolute devastation on Yeto's face after the fifth boss (Blizzeta).
** Although the reconciliation was [[CrowningMomentofHeartwarming heartwarming]] enough to make up for it.
* If you decide to play the talk-to-all-the-cats game in the Hidden Village, the cucco says that they have short memory spans (or something like that) and if you leave the village before you've talked to all twenty, they'll ''forget you were ever there''. This is clearly just meant to be a more creative way of saying "the game resets if you leave the area", but the way the cucco talks about how lonely the kitties are, coupled with the fact that they probably won't even remember playing with you can definitely bring one to tears.
** I'm pretty sure it was "short attention spans" rather than "short-term memory loss".
* When you return to Ordon village after being turned into a wolf, all of the townspeople are beating themselves up over how the children are missing, and Link is viewed as a monster.
** This counts as definitely in-universe for Link. If you don't manage to avoid Rusl, imagine how Link feels when one of his closest friends slashes him with a sword? If only Link would later, once human again, [[WhatTheHellHero point out that his wolf-self never moved to attack Rusl anyway and for all Rusl knew, didn't mean any harm.]] Not to mention pretty much all the [human] [=NPCs=] in the game treat Wolf!Link like a [[WhatMeasureIsANonhuman monster that has no soul]] ''when he just looks like your average wolf.'' Even if it's supposedly in self-defense, normally the player doesn't ever move to even use an attack near any humans, yet they still treat him badly.
** Coro, the man in Faron woods who gives you the lantern, is one of the only humans who doesn't freak out when he sees Wolf Link. He actually calls him a good pup or something to that effect, it's cute.
** He even lampshades the reaction Wolf Link gets from other humans. The other prominent one who isn't frightened by Wolf Link is Agitha, but she's... a little [[CloudCuckoolander funny in the head.]]
** Go into the [=STAR=] tent. Maybe he really is scared and just trying to make up an excuse, but the emcee at least ''claims'' allergies.
* When Link walks into Telma's bar for the first time after dispelling the Twilight, and Ilia looks straight at him and doesn't recognize him at all--the look on his face was likely pretty heartbreaking to some.
* More of a tearjerker caused by nostalgia, but when you open the door to the entrance to the Temple of Time and get hit by that music... thank you, Nintendo, thank you.
* During the final battle [[spoiler: when Ganondorf's giant glowing head is forming.]] The music returns as the fragments of the Fused Shadow surround Midna. Link, knowing what she's about to do, reacts in shock and begins to run toward her, reaching out, only for her to transport him and Zelda away with a smile.
** What's worse is right after the scene, Zelda and Link look around confused and then an explosion appears in front of them. Out of the dust appears [[spoiler:Ganon on horseback with Midna's helmet in his hand, strongly implying that [[SenselessSacrifice her actions were pointless.]]]]