Author's Note: Thank you for all the positive feedback, guys! Please keep reviewing the story and letting me know your thoughts. I am always open to constructive criticism of any kind. Also, as suggested by imastrawberryIchigo, I will refer to the human duplicate of the Doctor as Theta Sigma (his academy name) on occasion if there are future situations with the both of them. It should help with a bit of the confusion. (Side note about that: Since I have no idea where I'm going with this yet or if (possible spoiler alert?) the 11th Doctor is returning at all, it may not be needed.)
Rose played with her hands as she listened to the Time Lord talk about his adventures post-DoctorDonna. She bit her lip, saddened that she had missed so much. Eventually they fell into silence. Rose looked up at him and half smiled.
"Doctor, did you think about me? All those years, travelling without me. Did you remember me?" The Doctor took a deep breath.
"Always." He put his hand on Rose's knee. "I always wondered what you'd be doing, how you were." He paused. "I wanted to go to see you. There's something I never got to tell you, Rose." He looked directly in her eyes. "I love you."
She looked away. Her mind was spinning. She didn't know this Doctor, but it was the same man she'd travelled with. "I don't…know how to put this. I loved you. All that time ago. I fell in love with your big nose. Then you changed, and I still loved you. At first I wasn't sure, but I did. You were still you, just different. After you left me with him on Bad Wolf beach, I guess you changed again. And I guess that means you are still you… But I don't know you. Not like this."
The words hurt the both of them. Rose hated telling him the truth. The Doctor was reminded of the pain he leaves behind. He was reminded that he loses people as much as they lose him. The fate of he who lives forever is that he has more time to leave people hurt. And yet, with so much time, he still doesn't have enough to try and fix the damage he does. He studied his hands as tears welled in his eyes. Rose whispered to him, "I'm sorry…" He sniffled and looked up, flashing a half-smile.
"No, no. I understand. I should have told you when I had the chances. I let them pass, and in that I let you pass, as well. For that, Rose Tyler, I am sorry." She smiled at him through teary eyes. She put a hand on his cheek and pulled his forehead to her lips.
"I forgive you, Doctor." He pulled Rose into a hug. They sat on the couch hugging and crying until their tears ran dry. The Doctor stood up and looked at Rose. He had told her. He had finally stayed around long enough to see the damage dealt with. He walked back to the TARDIS and left without saying another word to any of them. He hated goodbyes.