Story I haven't read in over a decade now but it was a Ranma 1/2 / SM x over (with maybe other xovers in it it's been so long I don't remember)
what really sticks in my head about the story was a conversation with Pluto where she remarked something along the lines of 'back then we were an interplanetary empire we never stood a chance' and 'this time we're a group of plucky young girls we can't loose' but beyond that I can't remember anything else about it anymore I know it's not much to go on but that conversation has been partially stuck in my head for years so every once in awhile I try looking for the story again and get frustrated when I can't find it
I've asked elsewhere recently and they suggested I ask here and to save some time I will list some of the ones they thought might be it but weren't
The Girl Who Loved and its sequel Violence Inherent in the System
Desperately Seeking Ranma
Harry Potter - World Traveller.
At the time I read it I didn't realize why the conversation stuck with me so well but now I think back on it and think perhaps it stuck with me so well as it seemed to be a star wars reference because twice the bigger empire was defeated by the smaller force first the nominally 'good' empire fell to the smaller evil one then the large evil empire fell to a small force of freedom fighters