SPOILERS FOR MAHO SHOJO MADOKA MAGICA
Darkness is promised and darkness is given in Maho Shojo Madoka Magica, every episode digs further down and it doesn’t fully pull itself out in the end. Besides Kyubey, Homura was the most ready reflection of this very tone. When we meet her she is single-minded in her pursuit to stop Kyubey. She doesn’t communicate her reasons and refuses to explain the situation instead insisting things just are as she says. Then we finally learn the truth of who Homura is, a girl who has repeated this story over and over, she has been here countless times before and it has changed her, which only intensifies the weight she carries. Because of that, the Homura we know now is a girl consumed with Madoka, everything else is irrelevant. What originally started as selfless became almost selfish. Homura stopped understanding who Madoka was, what she wanted, or what would make her happy; she became simply obsessed with her goal of making sure Madoka never became a magical girl.
Obsession is not love; it is not friendship. But often times it is born from them and the complex desire to protect. It is a spiral, just as Homura’s wish is a spiral.
But in the end Homura’s obsession created the circumstance in which Madoka had enough power to change the universe, history, and time itself. Still, I wish they would have addressed some of Homura’s flaws in the final parts before absolving her of them. Instead of Madoka saying “You’re my best friend,” what I wanted was acknowledgment and forgiveness, why not something more like “I wish we could have understood each other. Thank you.”
Reverse Thieves 
“Obsession is not love; it is not friendship. But often times it is born from them and the complex desire to protect. It is a spiral, just as Homura’s wish is a spiral.”
You’re forgetting she became “obsessed” because Madoka asked her to save her. Madoka at end understand this, so she knows Homura doesn’t need absolution, because she’s not to blame to begin with. Instead, it’s Madoka who apologies to her, for making her go through all this because of her selfish request (to be saved).
I do not remember that part, but that is excellent! There was certainly a running theme through the series about the best of intentions and also not realizing how your wish will affect others.
-Narutaki
It happens in one of the timelines.
At first, Homura repeats time out of her own volition, out of a desire to save the girls from tragedy.
In the 3rd or so timeline, Madoka and co. all find out about the soul gems and despair before fighting Walpurgisnacht.
It’s the scene where they’re both about to turn into witches, and Homura said it’d be fine if they both turned and wreaked havoc.
Then Madoka cleansed Homura’s gem with the grief seed, and told Homura to go and keep trying to save her from making the mistake of becoming a Magical Girl.
Madoka asked Homura to prevent her from being fooled by Qbey, and not just saving her.
Similar, but not the same.
Homura’s main mistake was to reinterpret Madoka’s request into preventing her from making any kind of wish, rather than enlightening her about the Puella magi system and give her a choice.
Yes. I really felt Homura’s lack of communication played a big role. I mean 3/4 of the way through I just kept wanting to shake her and say “JUST TELL THEM WHAT YOU KNOW!!!”
-Narutaki
Thank you!I found this 9 months after it was posted, but finally someone who addresses this aspect; I was starting to wonder if no one in the fandom caught on. Even from the first timeline there was just something obsessive about this so-called friendship. Both Madoka and Mami died, but Homura only thought of Madoka when making her wish. And yet people hail it as the greatest love in the world.
Well I sort of disagree and do not agree. I viewed Homura’s story as one of the noblest that I have seen in a while. It was rare that I felt this much for two fictional characters and started tearing up in episodes 11 and 12. I found her to be making the ultimate sacrifice. Going through an endless maze to save her dear friend and find the way out.
Also as noted above it was born out of Madoka’s dying wish in one time line. Also just some fun trivia. The opening theme connect is sung from Homura’s perspective. If you ever get the chance to listen to a translated version pay close attention to the lyrics and how they relate to Homura.