Disclaimer: Let's just say Rebellion would be quite different if I owned Madoka Magica.
Once, the incubators hadn't allowed the puella magi a chance to regain their lost magic. They would fight until their soul gems were corrupted, and then they would become witches.
It had been the work of an insane incubator, one who called herself Henan, that changed this. She had been cursed with the emotion of curiosity, and had changed the system so that the puella magi could live longer. Their emotions were even more tormented. They had hope, hope that turned into a far more bountiful despair. And thus it was like this for countless eons upon countless eons, before a girl with unimaginable power, not that incubators could normally imagine, had turned the system on its head. But she too suffered. They all did.
A/N: Henan comes from a bastardized version of a translation of the Chinese word for incubator.