First let’s go to the specifics of Homura and Madoka’s respective wishes.
Homura: Redo her meeting with Madoka in which she is the one who protects her.
Effect: She enters a time loop where she gets a chance to save Madoka
Madoka: Wishes to destroy all witches of past and future before they are born
Effect: Every Puella Magi who sank to despair never became a witch and a new system of gathering energy was born.
Now, what I would like to discuss at this point is how Madoka’s wish intersected with Homura’s, leaving the question as to whether or not Homura’s wish was fulfilled. In order to drive my point, i’ll be basing it all on a character’s “informed choice”.
If anything, Puella Magi Madoka Magica has shown us the naivety of little girls. This is not an offending statement, this is simply the truth of this anime.
These are all noble wishes, even Mami’s wish to live on alone, but you have to admit, as reality dawns on them, these wishes are a product of their naivety. It is a price that they had to pay that comes back at them baring all fangs. Mami wished to live on but the fact that she’s all alone is payment for that wish. Sayaka wished to heal Kamijou but the payment for that is unrequited love. Kyouko wished for her father only for her entire family to be killed by him. Homura wished to save Madoka only to isolate herself. Most importantly, all of them wished without having complete knowledge of how Kyuubey’s system works and this factor sealed their fate in an endless chain of despair.
Then, Madoka finally made her wish. We can say that this is a carefully worded wish meant to carve the future of Puella Magi, filling it with hope rather than continuing the cycle of despair.Let’s analyze further what that wish mean and the effects that it had.
By taking on the despair of every Puella Magi across time, the system was rewritten and the universe, reborn and the memory of Kaname Madoka was removed from the characters of this anime save from Homura which was able to accompany Madoka to what I would like to consider as God’s realm (In Star Wars , Madoka has become one with the force :D )
We can also assume that from her experience of having a personal encounter with the divine (Madoka), Homura has inherited some of her powers.
Due to a timely explanation coming from Steins;Gate the altering of memories so that Kaname Madoka did not exist made sense but I am quite curious as to why Tatsuya seem to have remembered his sister.
With Madoka finally getting her wish, we seem to be forgetting another important matter.
Was Homura’s wish granted? Not really. But we can say that Homura finally accepted it and decided to end it.
The reason why she wished to go back and redo her meeting with Madoka was because she didn’t accept her death. This time, it’s as if Madoka has finally told Homura to stop what she’s doing and let her embrace her destiny.
Madoka was destined to die and Homura, from the first timeline never understood that. With how Homura became informed during the course of her time jump, she grew in character and came to understand how things were meant to be and with her acceptance, along with Madoka’s deus ex machina, she was freed from the curse of her time travel yet.
I would like to note here the irony that, despite wishing to protect Madoka, in the end, it seems that Homura cannot defeat fate.
Madoka was destined to protect Homura and until Homura acknowledges that, she’d never escape the time loop. And to beautify everything in this finale, what better way to remind Homura that Madoka will always protect her than to give her her powers. The bow and arrow that Madoka uses as well as those pair of wings are a reminder of Madoka’s love and self-sacrifice. If there is a second season, I believe that Homura will be a symbolic reminder of how one Puella Magi saved the future of all Puella Magi out of love.