So this just popped into my head. Nothing recognizable belongs to me. This is my version on what the doctor was really feeling. It's definitely 9/Rose centric. Au kinda. Hopefully you don't hate it. Please review.
After 900 years of traveling he finally understood why he had the urge in the first place. Time Lords always felt their pull differently but none were ever dragged off planet and through time. At first he just chalked it up to being a renegade, unable to watch innocents suffer and having a thirst for adventure, and simply ran through time.
When the Time War raged, he tried so hard to stay out of it but secretly wondered if his bond mate was suffering. The very thought made him want to double over and retch violently. When the time came to end it, he mourned for days what he thought was lost.
He regenerated and lost all hope and will to live. So it surprised him when he felt the need to stop on earth one more time. He rationalized it by telling himself he would go out saving something instead of leaving behind only destruction. When he found the autons and the living plastic he thought that it was a perfect set up and then he found himself in the basement of a department store.
As soon as he took her hand he knew that he was in trouble. He had found her. After he shooed her out of the building to save her (because he couldn't stand her being in danger) he finished setting his charges he realized he could no longer go out with the store. So he ran.
Soon after he realized that he had not taken out the source of the problem and that his pull was still in danger. He traced one of the arms to her house for Rassilon's sake. Once he saw her again he knew that though he wanted her with him, that he had to give her the chance to get as far away from him as possible. It would kill him to walk away from her but she would be safe.
He didn't expect to see her again after he warned her to forget about him (though internally he was crying for her to recognize that it was not what he wanted) but his jeopardy friendly pull just wouldn't stay safe. He almost had a heart attack when he saw her sitting across from the plastic version of her boyfriend.
She was very calm finding out that he was an alien but he couldn't be sure that it wasn't just the adrenaline from almost being killed but living plastic. His TARDIS recognized her pilots pull instantly and made the small hop across London interesting. He also found out that his pull was fairly smart and a quick learner.
When the Nestene Consciousness started raging he was terrified. Terrified because Rose, his brilliant pull Rose, wasn't running. All he wanted was her to be safe instead she saved him and the world. He could no longer stop himself and he asked her to come along. He was devastated when she said no and left quickly to try and hide his hurt. Soon enough he realized that not only had he not told her everything, he could feel the pull bond and over it came the feeling of regret. He realized that she must really be questioning her decision. Almost as soon as he landed (not 5 minutes after he left her and he thanked the TARDIS for making sure he got it right) she ran to him. He couldn't have ever imagined being happy again let alone this happy. Even if they never completed the bond he was perfectly fine with just being in her presence almost constantly.
So what did you think? Should I continue it? I can't really decide at the moment. Thank you to anyone who reads this!