Disclaimer: I don't own Bleach.
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When Rukia gave Ichigo her powers to save his family, she knew what she was doing was wrong but she did anyway. She didn't know him and he didn't know her, they didn't know each other at all so why is she helping him? Is it because it's her job? She said that she'll protect those who she cares about but she didn't know him then, did she? She doesn't know the answer.
A few days after the incident, they came to get her and kill him. They told him that what she did was a crime and he couldn't believe what he was hearing. They killed him, but he survived thanks to a friend. Rukia's powers were gone but his are deep inside of him even though he doesn't know.
She trusted him; he trusted her and that trust will never break. They were friends and that shouldn't change whatever happens. Even though he doesn't show it, he cares for her because she helped him save his family, but is that the only reason why? He doesn't know the answer to that.
When she was gone, he realized that he was a fool for not realizing that this might happen. He realized, he only cared for and protected everyone else but didn't for the person who gave him the power to do that. Did he?
He realized that she cared for him. She ran away to protect him because she knows that they'll be after him. He realized that he made a big mistake. This wouldn't have happened if he was more careful, stronger.
He promised to himself that he'll get her back. He'll risk his life for hers because it was his fault that she got in trouble in the first place. He knows that she'll do the same if she was in his shoes. When they meet again in the place where she is, he wants to ask "Rukia, do you still trust me?"