Madoka opened her eyes, staring up at the grey sky. She felt tears running down the side of her face. She had defeated Walpurgisnacht, but what was her effort worth? The city was gone. She had seen the shelter where her family and everyone else was hiding, and witnessed the giant witch's power crush it in a single blow. Everything she cared about was gone.
She remembered the last time she saw her mother. She had been wished well, and let to run off and find her friend amid the storm. She remembered her father, who must have been waiting for her to return when everything ended. She remembered her brother, probably only concerned with finding out where his sister was so they could play.
She tried not to think about them. Where are my friends?
Hitomi and Kyosuke had been in the shelter as well. They were gone. She'd never see them again.
Or Mami. Poor Mami who now rested in the void inside some long-vanished labyrinth, fallen prey to a witch.
Kyoko. Sacrificed herself to protect Madoka from a witch that had once been...
Sayaka. She had given her everything for what she believed was right. Even her soul. Now she was gone.
Madoka cried, sobbing loudly in the rain. Homura... the dark-haired magical girl had disappeared between two buildings tossed about by Walpurgisnacht.
Walpurgisnacht was gone, but she was too late. Everyone was dead.
And soon, everything else would be destroyed too.
Kyubey smiled down at her, perched on the broken stone that might have been an overpass once. "You're turning into a witch, Madoka. With the energy you are about to create, I will have more than filled my quota for this planet. I wish I could stay to observe the destruction your witch will cause, as I'm sure I would be able to learn quite a lot, but I have to hurry on to the next planet. I have a surprisingly long queue."
Madoka, feeling her soul turning black, reached up her hand towards the incubator. "Don't you... understand? You f-failed... When I turn... into a witch... it will be too strong. It will destroy the whole world."
Kyubey nodded. "Regretful, but your race has served its collective purpose in the survival of the universe. I thank you for that, as do the countless souls that are free from the threat of entropy. However, my work continues."
"No!" Madoka winced painfully, stabbing hurt shooting through her body. She gasped, trying to find the words to make the small alien understand what she was saying. "It won't stop! It... it will consume the world, and... and then it will just keep growing, and then it will destroy everything else! You've doomed my world, Kyubey... but more than that, you've doomed yourself... and everyone... and everything... in the universe."
In that last moment, right before Madoka's tiny little body erupted, Kyubey's ever-present cat-like grin dropped into a frown. "Oh."
His body, mind, and soul were shattered by the massive witch as it shot into the sky, darkness spreading in all directions.