Time heals all wounds, and yet it takes a while for you to get there.
Homura knows that very well, and understands that it will take a while for Madoka to smile again - that carefree and warm smile that made Homura feel that everything was all right with the world.
(There was a time when all it took for Madoka to smile was just having Homura by her side.)
She misses that smile. Most of all, she misses seeing Madoka look happy, and Homura - because she's a simple man when it comes down to it - really yearns for nothing more, but for Madoka to be happy again.
But Madoka isn't a child any more, and Homura knows that things will never be as simple as they once were.
(She can't just soothe Madoka with half-baked truths anymore because Madoka has begun to understand how the world works).
Yes, Homura is at side now, but Madoka often gazes at her with a look that's asking her just what kind of price they had to pay for being together. Sometimes, Madoka looks so sad and guilty that Homura resolves to not leave Madoka alone for a second.
(The truth is that it's not only Madoka who lives for Homura, it works the other around too.)
Homura tries to be there for Madoka as much she can. At night, when the dreams get too bad and Madoka cries out, Homura embraces Madoka, promising that she'll never leave.
(And she won't. Homura is a woman who keeps her promises.)
"Don't you think it's selfish of us to be happy when they're all dead?"
Madoka asked on one occasion, and Homura frowns - not because of the question, but the fact that Madoka's eyes are sad, full of self-hatred and despair. It hurts Homura to see Madoka like this, it hurts because she knows she can't chase those bad feelings away.
(There is blood on Madoka's hands, and it will never wash away.)
Homura wants to tell Madoka that it's fine to be happy, that they would have wanted it, but she knows that Madoka will not accept that as an answer - not yet because it's still too early. So Homura can only pull Madoka closer to her, stroke Madoka's hair, and tell her, "No, maybe it's not. Maybe it's even selfish. But it's human to be selfish, Madoka."
And Homura is a selfish woman, she knows that very well.
Because, though she never tells Madoka, Homura wants Madoka to live because she needs her; needs her so much that she doesn't care about the rest. So much that, even if Madoka wants to die, Homura won't allow her to.
(If Madoka died, Homura would die too).
And so, Homura will wait for the day that Madoka smiles again.