Nintendo's titles tend not to lean hard into narrative, yet there are nonetheless moments of emotional poignancy; which one(s) resonated with you the most, and why?

The tragic tale of the Flute Boy's fate and his father always comes to mind for me:

Super Metroid, Ocarina of Time, Majora's Mask, and Tears of the Kingdom spoilers ahead:

Baby Metroid's sacrifice, realizing Saria actually died, Deku Butler crying over his son, finding Zelda (the light dragon).

Twilight is Nintendo's best narrative. Lots of parts to pick but probably when Zant takes Midna's power.

I guess this is an open spoilers thread.

The ending of Xenoblade Torna is heart breaking. Mythra kinda causes many people to die including a titan in an ironic twist trying to protect them.  She is so traumatized with so much death she develops a split personalty and becomes Pyra. She meant well but her actions meant she was too dangerous so she was sealed away by Addam(Rex finds her 500 years later in Xenoblade 2). Jin with his blade users death was losing the only thing that mattered to him. It makes sense why he is a villain in Xenoblade 2.

Oh, man, the whole hyrulr thing in wind waker, the castle section was quite moving.

Yeah it's been a while since we've had a Ninty game in this category so I figure spoilers for old games is fine.

Man, I forgot about the Xenoblade games, that opens up some real heartbreakers, especially in 3.

Mother 3 should be #1 by a landslide i guess ?
(Subtle: Fassad's identity reveal. Obvious: The final battle)

Special mention : Majora's Mask though it's difficult to pinpoint an exact moment

Eternal Darkness

Fear is an emotion

Link’s identity reveal as a Hylian (rather than a Kokiri) was something that got me in OoT. I remember it just hit differently at that point, 30 years ago.