well I guess with a real fan-fic, you have to concentrate on the character or group of characters you would most like to tell an untold story of, and then from that point just try and write it like you would any other story, preserving things that are "true to character" to whatever degree you want
really, you can reimagine a character any way you want like say a "What If?" story...but if you want to be true to character and maybe even unofficially fit it into the chronology somewhere that would require more research I suppose
honestly I don't think there are any rules or formulas too it, everyone writes differently
stretch your ideas out, find how they intersect then build off of that. my fan-fic is nearly done and pretty well put together and all the cool ideas I started with seemed so chaotic and hard to get down on paper. it'll all be okay.
P.S. Check out "Batman Dark Utopia" on the fan-fic board.