MotivationWithout a doubt, Naminé's strongest motivator for the first half of her existence is feelings of loneliness and a fear of being along. As I have previously mentioned, Naminé has no memories from Kairi and therefore does not know who she is. Unfortunately, Organization XIII found her and took advantage of her lack of identity in order to use her powers. They had no intention of considering her an equal; her role was more of a hostage than a member. With no friends or people that cared about her existence, Naminé spent her time alone unless she had the misfortune of one of the Organization members visiting her. She was nothing more than a caged bird that had no idea what it was like to be free. It's no surprise that she was overwhelmed with feelings of loneliness. When threatened with the idea that she would be locked away in Castle Oblivion forever if she did not obey Marluxia's every order, Naminé had to comply. She did not want to; she felt guilty about doing something to hurt Sora and his friends, especially as she saw how hard he was trying to protect her. The fear of never escaping the feelings of loneliness that she was drowning in was just too much to bear, though. Even if she had to hurt someone and do something she knew was wrong...as long as she could be free from her loneliness, she would endure it.
Or so she thought, anyway. After being freed by Axel, Naminé realizes that she has to make a decision. Her window of opportunity would not be long before she was found by Marluxia or Larxene and therefore she needed to act quickly. She had the choice to remain where she was in order to have a chance of freedom but watch Sora slowly be destroyed, or to go to him and set things right. Her feelings of guilt ultimately were so overwhelming that they triumph over the loneliness than ran so deep. She realizes that she had been incredibly selfish and her loneliness was not a good reason to hurt someone else. Once she tells Sora the truth, her primary motivation begins to change.
After gaining Sora's forgiveness, a combination of her feelings for him and a desire to atone for what she did becomes the driving force that replaces her fear of loneliness. Naminé deliberately disobeys both Larxene and Marluxia, no longer caring what happens to herself. She also chooses to give Sora the option to forget her and his memories of Castle Oblivion in exchange for getting his true memories back. I personally feel that her offer is a big step away from her previous source of motivation. Sora had been the only one to actually care about her and not think of her as a disposable tool or a "witch." With him by her side, she would no longer be alone. Not only does she give him the option, but she respects his wishes and does everything in her power to take care of him and restore his memories while he is asleep. She is clearly upset that he chose to forget about her, but she pushes forward. Naminé commits herself to making things right for the rest of her existence separate from Kairi. She works mostly behind the scenes and although she is now working on her own accord, she is still alone. DiZ still showers her with remarks that nobodies should not exist and implies she is disposable. Even so, Naminé pushes forward because Sora has become more important to her than herself.
Though secondary to her desire to set things right, I think another important motivation Naminé has after the events in Chain of Memories is to meet and act as a guide for those in a similar situation to herself. She seems to care about both Roxas and Xion's feelings and opinions even though she knows they need to disappear in order to make Sora whole again. I feel that Naminé probably sees a little of herself in them. They want to be acknowledged and be with people they care about rather than only being seen as part of someone else. They want to find a purpose other than returning to their counterpart because they were not meant to exist. Naminé knows what needs to be done and prioritizes Sora's recovery over everything else, but she also cannot help but feel compassion for the both of them because of how similar they are to her. Therefore, I think part of her drive to make sure Roxas and Xion both understand everything before they disappear stems from her empathy. I think it is also possible that Naminé feels like her helping them in a way no one else really can creates some sort of meaning to her existence. She would not just be a girl who followed orders and tampered with an innocent person's memories, only to realize she was wrong and fix things. I believe that Naminé wanted to do something good of her own accord as well.