A great many fics involve the return of Dark Danny. This is largely due to his immense popularity as one of the show's best villains, and because his episode ended on a Sequel Hook that was never followed up on due to the show's cancellation. What he does in these fics varies from story to story: sometimes he gets shipped, other times he gets "redeemed," but he usually goes on a Roaring Rampage of Revenge.
Fics that diverge from the events of The Ultimate Enemy, where Danny still manages to defeat Dark Danny, but the latter still succeeds in killing Danny's family and friends due to Clockwork not intervening to save them. As such, Danny must live on alone, but armed with the knowledge of what created Dark Danny, works to avoid the same mistakes. This usually involves him never going to Vlad, instead moving in with another student (usually Valerie) and trying to recover from the traumatic event.
"Reveal fics" where somebody, usually Danny's parents, discover that he is half-ghost are pretty common.
There are two main varieties when it comes to Danny's parents. The first usually has Danny having to save their lives, exposing himself in the process. The second, known in-fandom as "dissection fics", appropriately have his parents capture him and attempt to dissect/torture/kill him before the reveal is made, hence the nickname. Depending on how dark the story in question is, the reveal only occurs during or after vivisection.
Often tied up with the second variant are fics where Jack and Maddie Fenton get calledout for their approach to ghosts being unscientific. Given that they pride themselves as scientists, it almost always triggers a My God, What Have I Done? out of them to realize how much harm their biases have caused, especially to their own son.
Reveal fics focusing on other characters are more likely to have other plots, such as Mr. Lancer's concern for his mysteriously troubled student leading him to discover the truth, or one or all of Danny's classmates getting trapped somewhere with him until he has to use his powers in front of them.
As the ghosts are, well, ghosts, many fanfics deal with their lives as humans and their premature deaths. Ember in particular has a lot of these, with many being some level of Song Fic using lyrics from "Remember".
It's pretty common to see fics detailing what happened in the first month after Danny got his powers, since the show doesn't.
Similarly, there are multiple fics that explore the circumstances and aftermath of the original accident, since the show doesn't show much of it in its original context.
There are also many fics which explore the nature of ghosts (either through the lens of Danny's ghostly nature or not), their society, and/or the Ghost Zone.
As Danny's human friends Tucker and Sam are exceptionally contentious characters and the plots involving them generally considered pretty uninteresting compared to the ghost happenings, there exist quite a few fics where their friendship with Danny ends due to a misunderstanding and he embraces the ghost side of himself full-time, often falling for one of the ghost women such as the aforementioned Ember. It's about 50-50 whether he ends up forgiving them by the end.
A popular category of fics revolve around Danny unknowingly becoming the new Ghost King after beating Pariah Dark. These cover a wide variety of common plots themselves:
Him being the Ghost King meaning that he can now be summoned, be it by some random person or a crossover character. If it's a crossover of some sort, then it's usually the villains or cultists who summon him, but occasionally heroes do too.
The summoner in question is usually trying to summon Pariah Dark and is understandably shocked to see a 14-16 year old kid instead. Danny will try to write their confusion off as claiming to be the Ghost King's secretary to help hide his identity.
Stories about his coronation, with Danny being a Reluctant Ruler who often complains about the job title. They often include the reactions of his friends and family as well.
Explorations of ghost politics and Worldbuilding with Danny actually trying to improve the Ghost Zone in his new position.
AUs where Danny dies and becomes a ghost completely. Can happen in any number of ways, but it's usually by some kind of accident, murder, or where something went wrong with the ghost portal and it outright killed him instead of turning him half-ghost.
Stories where the GIW finally get a hold of Danny and, even with the revelation that he's half-human, zero qualms about torture or human experimentation.
