Downfall, a story in three acts:
Betrayal - Drama/Angst
Revelations - Sci-Fi/Horror
A Distant Shore - Fantasy/Romance
Darkety-dark-dark.
You can trust your friends ... right?
http://pishoque.net/brian/fanfic/downfall/
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Updated -- and complete.
So, after reading this again (originally on FF.NET), I suppose I should throw some thoughts out there.
Part 1 seems very straightforward; setting up the characters and the situation.
Part 2 is where characterization might go askew. Koizumi is appropriately devious and wields a lot of influence over Haruhi, but I suppose that's b/c she lets him in fear of herself. I'm not fully convinced of his motivations; I can see him being jealous of Kyon, wanting a relationship with Haruhi (seen in Disappearance-verse), and being worried about the world, but taking the step of offing Kyon still seems a bit much. I suppose if you mixed those three ingredients together and Koizumi developed a sort of... oracle/high priest mindset, it could be possible. But, overall, only a small jump in characterization.
Haruhi doesn't seem too divergent from my expectations. Maybe a bit unobservant while little Haruhi is bossing Kyon around and a tad vengeful on Koizumi (it might be a bit more than he deserves, but punishment levels tend to be personal).
The first thing I think about Part 3 is that it is clever, incorporating the "remains" of the Disappearance-verse. As to the relationships, they seem to make sense. Often times relationships are a matter of opportunity, and in this case Mikuru had the opportunity and Haruhi did not. I'm not sure about Yuki, but it isn't dissonant at least. As to Haruhi's reactions, it seems that since she's been without friends for so long (and she was "just" betrayed by Koizumi) that she'd gratefully latch onto any chance for old friendships.