Madoka becomes pregnant with Homura

Homura's head resting in the lap of Madoka. Homura talking about several things, Madoka nodding along as she listens to the pain she went through.
"I couldn't accept a world that allowed someone as kind as you to be treated so cruelly. But even more, I couldn't stand that you'd give your life for such a world."

Madoka can't help her since her powers haven't fully returned, and only with her death with the Law of Cycles return. She takes Homura's cracked Soul Gem, and places it in front of her stomach, absorbing it's essence.
Homura asks how she can still care for someone who has hurt her so much, but Madoka replies it's because she knows Homura loves her so much. She wants to give her a good life so she can see the world with new eyes. She wants to be the one who protects her and gives her a new life.

Madoka carries the baby to term, with her family, Kyoko, and Mami helping her in turn.

Eventually Kyoko and Mami pass on, it's explained that the Law of Cycles split from her is independently working without her, however, she'll need to join up with it someday.

As Homura reaches 7, Madoka is working as a relief worker, helping people suffering from natural disasters. Gets to finally have a drink with her mom. It's gross, but she loves to be able to drink with her mom.

"It's your mother. Someone who was dumb enough to love a bumbling fool like me, and protect me from hurting myself."

"I wish I could've met her."

"When I look at you I see so much of her in you."

Finally Homura reaches 14, she's a bit rebellious, wondering who the hell her dad is, and why she doesn't have one. Madoka explains that Homura is her dad, but she says that's not possible, they told her at school it wasn't possible. But Madoka says it was.

Homura cries in her bed, and Madoka comes to comfort her. Patting her head.

Eventually Madoka is taken by The Law of Cycles, leaving Homura w Junko as her guardian now. She still feels resentful towards Madoka for leaving her, but can't bring herself to hate her. She constantly wishes to see her again. Kyubey eventually comes, wary but deciding to help.

Wish to Kyubey that she wants to see her mom, and granted with one final vision of her.