Hello Madoka Magica fans. I am YellowPearl07 for those who don't know me. I have re-watch Rebellion and then an idea came to my head. What if Homura did not became the devil/akuma? What if the Incubators were not completely destroyed? It lead me to write this. I do not own Puella Magi Madoka Magica or their characters, just my plot. I hoped you enjoy reading it.

Chapter 1: The Captured Goddess

Finally, Homura can see Madoka again. As Madoka descended from the sky, the carriage Sayaka and Nagisa are in is driven closer to the Earth. Sayaka is driving the carriage as Nagisa is blowing bubbles.

"Now, let's go. We'll always be together from now on." Madoka told her as she was closer to purify her tainted soul gem.

Suddenly, red crystals popped up on the ground as Madoka is taking the grief from Homura's soul gem. The red crystals started to shocked Madoka, interrupting the process.

"Madoka!" Homura exclaimed.

"W-what is going on?" Sayaka asked in alarm as the carriage began to tipped over causing both her and Nagisa to fall out of it.

Mami summoned her percussion-lock rifled musket while Kyoko summoned her spear.

"Did you thought that you have gotten rid of us completely? Human thoughts are so irrational...to think that you could win." Kyubey spoke out loud as many red eyes glowed in the dark.

"Incubator!" Homura exclaimed in disgust.

"Really, did you thought that it was over? You didn't even know that you were the bigger trap set for Kaname Madoka, speaking of which, those crystals were set up to capture the goddess of this universe. We have this planned out just in case if the isolation field was destroyed." Kyubey explained.

The red crystals continue to shock Madoka as she screams in pain.

"It's too much! These crystals...it's taking my powers away!" Madoka screamed. She started to fall as she disappeared in a flash of light in front of Homura.

"Madoka!" Homura yelled in disbelief.

Kyoko pointed her spear at Kyubey. "What do you do?! Where is she?! Where did she go?!" she demand angrily.

"Those crystals absorbed her powers, but don't worry. It will just cause her to be unconscious for a little while so don't waste your time fighting. She is already in our care. As long as she cooperates with us, nothing will harm her." Kyubey told the girls with no care at all.

"Why you little-" Kyoko began as she attempt to attack him. However, he disappeared before her spear could land a hit on him, along with the other Incubators.

Homura was on her knees, feeling devastated as tears fall from her eyes.

'It seems that no matter what universe I'm in, I can never be able to protect her just when I got the chance to do so.'

Homura opened her palm to reveal her cleansed soul gem.

"Madoka." she said her name.

Mami went to help Nagisa and Sayaka from the now broken carriage. Sayaka walked up to Homura.

"What are you doing? Are you just going to sit here while the Incubators have their hold onto Madoka? Who knows what they could be doing to her!" Sayaka asked her in frustration.

Homura said nothing. She felt that nothing could changed her back to the shy but happy girl she used to be. She is still the emotionless girl who have always suffered and it has only gotten worse. Just when she thought she could be happy being with her friends, but mostly Madoka, that happiness is quickly snatched away from her by those cold and selfish beings. She de-transformed to her school uniform as she got up to her feet.

"Akemi-san?" Mami called out. "Where are you going?"

"I'm going back...to Mitakihara City. After I am ready, I going to get Madoka back." Homura answered in an emotionless tone.

"But we have to stay together. Now that the Incubators have Madoka, we don't know what they could be doing next!" Sayaka exclaimed.

"You can do whatever you want, but I'm not coming with you." Homura countered as she continued to walk to the city.

"But-" Mami began.

"It's no use in trying to convince her. She won't give in. Seriously, she needs to start working together with us." Sayaka sighed as they lost sight of her.

"So, what should we do now?" Kyoko asked.

"We should probably head back too. Now that all of this has happened, we need to go back to the city. We can go at my place." Mami replied.

"Fine, but you are going to have to bake me a cake. I'm starving and I haven't eaten for a while." Kyoko complained.

"You're always hungry even at a time like this." Sayaka commented in disapproval.

"And Nagisa wants to eat cheese at Mami's place!" Nagisa exclaimed.

"Not you too..." Sayaka replied in disbelief.

-Homura's House-

At her home, Homura is still recalling what had happened. Despite the despair she is feeling right now, her soul gem is not blackening, whenever if this despair is just her in a bad mood or if it has to do with Madoka cleansing it, she does not know. She got up and went to her room to fall on her bed. A flashback of the time when she first met Madoka, her warm smile made her feel comfort, the first person to become her most dearest of friends. She touch the red ribbons on her head as she shed a tear.

"Madoka, I will save you. No matter what it takes." Homura cried as she fallen asleep.

-Incubator's Base-

In the base of the Incubator, there lies a mirror. However, this was no ordinary mirror for it has someone inside of it.

-Void-

"Where am I? What is this place?" Madoka asked herself as she walked around the void.

She was her human self. She is wearing a white dress and her short pink hair was down because she gave Homura her ribbons before she left. She wonder around the void until she saw a looking glass. She look through it to see her goddess self unconscious and the Incubator's base.

"No this can't be! That must mean..."

Madoka woke up inside the mirror! She saw that she is in her goddess form as she floats in this endless space inside the mirror.

"I knew that you'd wake up eventually, Kaname Madoka." a voice spoke suddenly.

"Incubator!" Madoka exclaimed in surprise. "Why are you doing this? Why are you causing all my friends to suffer!" she demanded.

"Because you are the key to our plan." Kyubey answered.

"What?" Madoka questioned quietly in confusion.

"We're hoping, now that we got you, we can turn the universe to the way it used to be. We are planning to have all the magical girls become witches again so we can collect the unlimited amount of energy. That way, it will be much easier than fighting wraiths." Kyubey explained.

"But that is just too cruel!" Madoka yelled. She hands pressed on the glass of the mirror.

"I'm afraid you won't have a choice. You can't get out of this mirror and even if you regain all your powers back, you can't break it." Kyubey replied in a emotionless tone. "When you are ready to help us achieve our goal, call us. We'll leave you alone for a little while." Kyubey told her as he and the others left her alone.

Madoka fell to her knees as she started to cry. She was starting to feel useless again, always depending on her friends to save her, especially Homura.

"Everyone... Homura-chan... I'm sorry. For causing all of you the trouble in rescuing me." Madoka wept inside her glass prison. "I'm so sorry."

That is all for today. Write, Comment, and Review if you want. It will help me know if you want to see more of my story. I hope you have enjoyed the first chapter. I'll update this story for every third week. See you at another time.