Author's Note: I don't own anything from Madoka Magica, it belongs to Shaft. I do own this story though.
Madoka had bid her farewells to Homura and returned her to the world. Now, it was time for her to remake the universe. She was not going to change much. First, she would remove the wishing system. Then, she would make sure that humans would still advance without it. Without that horrible system, all girls would be safe from the despair of being Puella Magi.
She was about to begin her work when something caught her attention. Being in all of time and space was new to her so she didn't notice it at first. She willed her concentration to focus on that one point.
Her spiritual body was now on a barren piece of rock. There was only a single star in the sky. It glowed red, a red giant. It was the only star left that still gave off heat. Even it only had a little more left in before it too was gone. She could feel only a single life force here. She made herself a bit more solid. A wraith of a girl drifted invisibly through the ruins of what was once a beautiful city. Without a single step she passed through streets and buildings.
Her destination was a laboratory. Without being able to put into words what anything there was, she still knew what the purpose of each instrument and tool. There was a single small white creature working.
The little white creature was the last living being left. Someone used to having many bodies only had one. She had been told once that emotions were considered a mental disorder to his kind. Now, she felt the fear and desperation that finally was overwhelming him.
"You never felt anything for those girls, but you really were trying to save the universe." Madoka gave a soft smile. "Not even you deserve this despair."
Insubstantial hands reached out to comfort him. His face looked up and turned away from his work. Red eyes stared right at where Madoka would have been if she were solid. Madoka smiled at him. The creature turned back to his work. She could hear in her mind as he talked to himself and tried to work out a solution.
Madoka let herself fade out and went back to her own work. No, she wouldn't remove the Puella Magi. She would not allow it to exist as it once had. There had to be another way. Slowly an idea formed in her mind. The system would be allowed to exist mostly as it had. Now, instead of witches there would be a new creature that would be born directly from the despair of humanity of a whole. Yes, this would be better. They would drop something similar to grief seeds to let soul gems be cleansed. Then energy could be taken from these instead.
Madoka nodded, content. This was not perfect. Now she knew, that nothing ever really was. This new system would keep the Puella Magi as human, but would still allow the harvesting of energy.