I'm going to pull in an experience I had back when I was part of the Anime fan-fiction community. During the period I was involved, I saw each part of the community (I.E., stories about each particular series) go through three distinct phases:
1. Continuing the story
2. Self-insertion
3. Meta-story
The first phase is merely recognizing the original story, and attempting to continue the themes of the original story with the original characters.
The second phase has people inserting new characters into the story - most of the time, these characters were thinly-veiled idealized versions of themselves, like the DM with the uber-NPC.
The third phase had people writing a story in which either the characters recognized they were in a story, or in some way turned the story on its head. While this is not a fanfic, possibly the best example of the meta-story would be Neon Genesis Evangelion, which turned the giant robot story completely on it's head.
Spoilers for NGE:
In the traditional mecha story, a young boy with no self confidence, finds his own courage, gets the girl, earns the approval of his parental figures, and saves the human race. In NGE, a young boy with no self confidence becomes even more insecure, cuts himself off from the rest of the human race, pretty much gets the girl killed, his own father can't stand to look at him by the end of the series, and he's also responsible for most of humanity being destroyed.
Play up the conflict between Chaos and Order, and down the conflict between Good and Evil.
Heaven and Hell unite in a struggle against an Elder Pantheon (lovecraftian) that threatens all that exists. Solar and Pit Fiend fight side by side, old rivalries forgotten.
A second schism occurs in the upper planes, and Heaven wars with itself - with the loser being cast out. And the loser is not Evil, but Good...