Two in one day?! I know, that's crazy right?
Well, after having to disappoint myself with the last entry, I decided after seeing this question that I could undoubtedly answer it and it would be wonderful! I need to restore some lost confidence, besides.
No beating around the bush, no confusion about what the question could mean. Personally for me, the most heartbreaking scene to me in any YGO fic that I've read would have to be from
yllimilly's
Rite of Passage. I honestly don't want to spoil the heartbreak by naming the exact moment or pairing - because I want people to read it and feel what I felt. [Warning, main character is Mokuba.] If you really want to know, I guess you can take a look at the tags, but...
But this story was sad for more than one reason. Not only does it address the pains of growing up and the worst lessons that could potentially be taken from downfalls, but in it Mokuba goes through a development process that has been my fear about his character pretty much since the beginning of the series. It's wonderful writing, tear-inducing (at least for me it was) pacing, and diction that really allows you to feel what the characters are going through.
If you've ever had a moment while watching a film, one where you've spoken to the characters on the screen and told them "No, no, don't--please don't!", then you'll enjoy this. I bargained with the story for several paragraphs to stop, but it didn't and it was painful and goodness and cathartic.