She left him in order to find that him that was still willing to let her stay forever. She can't tell him that though. No matter how much it hurts she can't tell him the reason behind her actions.
"I looked for you for so long, Doctor. I didn't care which you I found. I just--I needed to find you. I'm not like Sarah Jane. I can't--I don't just adjust. And I don't just haphazardly fall in love with people. I tried to do that after Bad Wolf Bay and I couldn't. You're wrong. Maybe it was a parallel world but you're wrong. I couldn't be happy without you. I know because I tried it before. I'll find my own way back. Make sure I'm there for the important events but I'm not letting you leave me like that. Not when I can tell you don't want to."
Re: voice || Private to the Doctor and Rose
"I looked for you for so long, Doctor. I didn't care which you I found. I just--I needed to find you. I'm not like Sarah Jane. I can't--I don't just adjust. And I don't just haphazardly fall in love with people. I tried to do that after Bad Wolf Bay and I couldn't. You're wrong. Maybe it was a parallel world but you're wrong. I couldn't be happy without you. I know because I tried it before. I'll find my own way back. Make sure I'm there for the important events but I'm not letting you leave me like that. Not when I can tell you don't want to."