I find that using the RPG guide books helps me to formulate plots and characters in my mind. For instance, I'm currently putting two stories together: one is post DS9 where the Cardassians help the Bajorans rebuild their homes and world in general. Of course the Breen and Jem'Hadar still cause problems. The other is after Romulus is lost, the federation attempt to send aid for and surviving Romulans and the Klingons send ship's to conquer Former Romulan Space. Also a third story the Andorian Romulan War post Enterprise series
My Fan fic has a lot of sex. (OC) female human and part Yridian. Trust me, there's a reason. But I'm careful to keep the know characters, the TNG crew, in character.
Just remember, this is a family-friendly site. It's one thing to suggest characters have sex, it's quite another to graphically show that they have sex. As to original question about writing good stories: not say that any of mine were "good", but almost all of my stories started in my head with the end of the story. The moral of the story, or the punchline if it's a silly story. If it's part of a series, I'd wrap it up and leave a hook for the next story. I used to write in more of a D&D-type fantasy setting, but my whole collection is on a hard drive four or five computers ago. A few months after moving all my stuff to the then-new computer, I had to do a format-C / reload and lost everything.
Pfft. My Muppet fanfic has nearly all of the characters having sex in the first chapter. (Not to brag or anything)