author's note: Post-series/first two movies. Doesn't reference the third movie at all, since I haven't seen it yet.
Now Madoka was gone, or rather she had always been gone, but Homura still saw her sometimes. In the middle of a battle she'd catch a glimpse of pink movement out of the corner of her eye and momentarily forget about the wraith she was supposed to be fighting. The first time she actually saw her beloved friend's face, she forgot to breathe for the rest of the battle. Of course breathing wasn't really necessary with her soul gem, but it was a comforting part of maintaining the illusion she was still human, and so she usually tried to keep up with it. None of the others had ever seen Madoka, and they wouldn't know it even if they did. It had been going on quite awhile before the raven-haired girl realized she was only seeing her friend when she used her powers, and that's when she finally understood. Madoka had written herself out of history, but her spirit could still exist in these small universes outside of time, filling the lonely space that had previously belonged to Homura alone with her loving presence. They could be together again, in their own world, even if it was only for a few moments between the moments her magic had stopped. And for Homura that would be enough, until she vanished forever into Madoka's loving embrace, as all other magical girls before her had done.