Homura - the only one she will submit toKyouko seems oddly intimidated by Homura's skills even from the moment they met. Homura jumps in to stop a fight between Kyouko and Sayaka because she wanted to prevent Madoka from becoming a magical girl. Kyouko asks Kyubey about her, and when she can't get any information she states "I won't fight you since I haven't a single clue what hand you're gonna play. I'll back down for today." This is really unusual for Kyouko, and out of character. This instant caution that Kyouko displays shows that she may be a bit cocky in her abilities, but she also knows when to back down and who to not have as an enemy or an opponent. Homura came off a bit too intimidating for Kyouko to really approach in the same manner that she did Sayaka.
Homura hunts Kyouko down, spotting her playing DDR. Without even turning around, Kyouko asks her what she wants from her. Homura explains that she wants Kyouko to take the city for herself as the head magical girl because girls like her are fit to be magical girls. Homura goes on to explain that Sayaka is incapable of being a magical girl and that she is just going to be a burden. Kyouko asks Homura what she plans to do about Sayaka because she is hot-headed and will charge back in if nothing is done. Homura tells Kyouko she wants to end this as peacefully as possible, and tells her "Don't interfere. I'll take care of it." Instead of arguing it, Kyouko changes the subject to ask questions about Homura and her intentions. Homura tells her about the upcoming Walpurgis Night, and how she needs to take care of it before she can leave the city. Kyouko holds out a peace of candy and asks Homura to team up with her to take care of the night. Homura just stares at her, and the scene ends. Kyouko senses how series Homura is, as well as her powers. She is also intimidated by the fact that Homura isn't open to talking about herself, only the bare minimum of information is given out.
Kyouko, curious about Sayaka, is unable to stay away from her. She ends up trying to fight her once again, but is interrupted by Madoka and Homura. Homura tells her she is angry because she is doing the exact opposite of what they discussed, and Kyouko tries to play it off as a simple fact that she couldn't help herself. Later on, Homura visits Kyouko again and asks her why she is letting Sayaka take the kill of the witch right in front of them, when she is suppose to be the head magical girl. Kyouko tells her she is just watching the fight, but as soon as Sayaka starts to get hurt, Kyouko attempts to jump in. Homura doesn't understand why Kyouko is so interested in Sayaka at all. Kyouko continues to ask Homura for information about Sayaka, and why she acts so differently. Homura tells her that Sayaka's soul gem is very impure and that it's only a matter of time before something goes wrong.
Homura goes to hunt down Sayaka because Sayaka makes Madoka feel terrible. Homura's main goal is to make sure that Madoka doesn't turn into a Magical Girl, so she attempts to kill of Sayaka so that Madoka doesn't have to worry about her anymore. When Homura is about to kill her, Kyouko comes running in quickly and grabs ahold of Homura. Homura, shocked to see Kyouko, tells her to leave because she is interfering. Homura previously warned Sayaka to not harm or hurt Madoka, and she had failed in Homura's eyes. Kyouko doesn't let her grip go, and screams to Sayaka to run away. Sayaka listens and gets out of there. This is the one scene where Kyouko does something to defile Homura to an extreme. Kyouko realizes that Homura is a good person to have as an ally, but she also realizes that Sayaka means something to her. When it comes to ones she loves, Kyouko is willing to fight back and protect them. Kyouko later tells Madoka that Homura isn't her friend, just a person she teamed up with to defeat a tough battle.
We find out that Homura has the ability to stop time and rewind it if needed. Homura has seen Kyouko die countless of times, and she clearly cares about her. However, her main goal is to save Madoka. Homura is sad to find out that Kyouko is killed again by Sayaka's witch/sacrificing herself so Sayaka won't be alone, not only because she needs her help to defeat the Walpurgis Night. Kyouko, however, never learns this fact because time continuously gets reset, and she never finds out how much pain and suffering Homura has to go through each time watching her friends die over and over again. It's actually really a sad relationship that Homura has to have each time with her.