Suggestions in writing stories seriously? And some other writing advice requests...

I've been wanting to write an AU of MLP for a while, but one of the things that keeps causing me problems is humor.

In a first draft, which is extremely non-canon for it at this point, I was going to have a secret society (of the "wants to resurrect Nightmare Moon" variety, a plot point which I'm fairly sure won't happen at all now) having minor difficulties meeting up. This was going to include a number of references ("swordfish" as a password, getting the wrong secret society and getting most of the way through the authentication phrases before noticing, the guard going "Oh, you want that secret society over there" while pointing to a similar-looking ominous doorway, and the whole idea that Canterlot has THAT many secret societies), mostly from the wonderful work that is the Discworld. Unfortunately, I'm not Terry Pratchett (which you can also tell, because it says I haven't written anything...).

I was rightfully informed that it kinda sucked, and I've since realized that I might have a better explanation for things which also lets me use a different character. Unfortunately, I still have an easily-distracted sense of humor that wants to do things like the "My Hovercraft is full of eels" skit (at least with the serial numbers filed off) during calibrating the speech module (and then make a somewhat improper joke**, because my shipping tendencies are strong). Which is probably something that doesn't have a real need to happen, since there's no reason that spoilers* would even forget Equish, even if she did get her mind absorbed by SPOILEEEERRRRRSS to save her life after nearly dying on her run from The God-Empress of Ponykind (check your ancient teleporting artifacts, folks! They might be dangerous!) after nope thinks she's in trouble from her mentor.

So, that's another tasteless joke that should not be, but I'm trying to figure out what sorts of things are funny in a story, and which ones are stupid and break immersion. I'm fairly sure that the rule is that there must be a reason for the funny thing to happen, and not just throw in something entirely random*** (and worse unrelated to anything else going on) for no apparent reason other than because it's funny and my muse went and got sloshed**** without me. I also suspect that something like the aforementioned translation error is probably something that's never really fine to include unless it's a crackfic. Which is something that I'm probably not actively trying to write at the moment. I'd love to have some advice on what's normally included in this sort of thing.

However, as will be discussed later, there are a few other things that are probably stupid but that I can't as easily get rid of.

• Humans, at least way back in the prologue
• Potential crossovers with the Bolo-verse (not always a bad thing, but it's feeling a bit more like "for the hay of it" rather than useful, even if there is a purpose)
• Elements from the Mutineer's Moon-verse, specifically the moon-is-a-starship idea
• Elements from Safehold, namely the war that sent the ponies off on their own and also the fall of Dream Valley
• A cracky non-canon epilogue, where, after the ponies are released from their containment field, they make contact with post-book-three Mutineer's Moon-verse humans
• WHY Sunset manages to find the ship in the start of the story (Even with the intentionally unreliable narrator (think the Oceans movies or the original Now You See Me) I have no explanation for how it's there, or how or why she ends up there, but need it for the rest of the story.
• Probably more random stuff that seemed a good idea at the time

I'd also love to see examples of stories that you think are funny, or that have wildly funny parts, that somehow manage to make them fit well into the rest of the story.

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*It's totally Sunset Shimmer. Also, "spoiler" is a REALLY weird word on inspection. Spoiler, spoiler, spoiler... Hmm.

**Basically she makes an accidental innuendo, and then comments "Well, it's not entirely wrong, but certainly not what I meant to say..."

*** Something like the following:
Two stones for the pegasi under the sky,
Two for Earth ponies on farms for stone,
One for the unicorn not born to change.
One for Twilight on her crystal throne,
In the town of Ponyville where sanity dies...
Magic to rule them all, Loyalty to bind them,
Laughter to bring them all and in the castle find them...
In the land of Equestria, where sanity dies…
Yes, I wrote that myself. If you hated it... I still wrote it, unfortunately.

****I can happily say that this is something I've never done, but I have to wonder about my muse sometimes.