Doctor Who doesn't not belong to me. If it did there would be no need for this story because the Doctor and Rose would be together forever. So there. :) In other words, the BBC owns all.
D.O.C.T.O.R.W.H.O
As the Doctor and his friends flew the Earth back home he wished the trip would never come to an end. It was a moment of pure happiness and Rose Tyler was right here beside him. He dreaded what was going to come next, but he still enjoyed the moment to the fullest while it lasted. It felt great to have the TARDIS filled and piloted the way she was meant to be and to be amongst so many friends. Moments of such utter success and joy were so few and far between.
After saying goodbye to Sarah Jane, Jack, Matha, and Mickey the Doctor knew that it was time. His final trip in the TARDIS with his Rose. Their time apart may have given him time to accept not being with her, but it had not, nor would it ever, make it ok. She had been a perfect companion, a balm to his weary soul. Not a perfect person, but a person that fit him and what he needed perfectly.
The Doctor knew it would be harder on her this time. Harder because she had worked so long and hard just to reach him. She truly had wanted to return to him and fulfill the promise she had made to him to be with him forever. The depth of the love she had for him almost took his breath away. Being a Time Lord he knew there were things he could not change, and that even if he could, ultimately death would still someday separate him from his beloved. That allowed him distance from the situation even if it left his hearts in shambles. Rose might have understood it on a base level, but as she had not lived over 900 years, she couldn't completely comprehend it.
It would also be harder on the Doctor as well. Losing Rose for a second time was incomprehensible. He had never dreamed he would get to see her again let alone that he would have to leave her on the beach, again. But this time he wouldn't have to leave her alone. His metacrisis would be there for her but that would not be the same. He would not get to know the joy of being with her.
Landing back at Bad Wolf Bay, the Doctor said his final goodbye to Rose. Filled with love for her and wanting her to be able to move on, he released her. Now instead of telling her he loved her but was still leaving her behind, he gave her the gift of his double who needed her as much as she need him. He knew the path would not be quick or easy for them, but they would find a life together as long as it was what Rose wanted. No longer able to dance among the stars, at least for a while, they would be able to delight in being together instead.
Speaking of delighting in one another… the Doctor watched Rose throw her arms around the new Doctor and kiss him. If he thought it had been hard watching Mickey kiss her, or other guys pay attention to her, it was nothing like watching Rose kiss his double. How could somebody basically be jealous of himself? Yet the Doctor wanted to be the one to touch her and love her. He wanted her arms wrapped about him and her lips kissing his but instead took comfort in the fact that the emotion she was expressing was love that started with him. It still was not an easy thing to watch though so he turned away.
As one final gift, the Doctor did leave behind a piece of the TARDIS with his double so that he and Rose could eventually travel the universe once again. It would be awhile before that would happen, so there was plenty of time for them to grow together. Eventually though he was certain that the new Doctor would travel in the TARDIS with Rose Tyler. Just as it should be.
The Doctor stepped back in the TARDIS with Donna, his hearts and even his soul, feeling heavier than they had ever felt before. He'd said his final goodbye to Rose and now he had to do the same with Donna. The Doctor knew what was going to happen even if he had kept it from both Rose and Donna– a human brain simply could not survive the knowledge of a Time Lord. The relationships he had with Rose and with Donna were so totally different but both were essential to the man he was now. It was not fair that he should have to give them both up, in the very same day, but so much in life was not fair.
The only thing the Doctor could do was look forward. He would not, and could not, go through losses like this again. He would journey on, but the journey would be solitary because the Doctor could handle no more goodbyes. He couldn't bear a TARDIS that felt any smaller on the inside.
A/N: Well there you go. Obviously I decided to go with the deleted TARDIS coral scene since I love it. Not totally satisfied with what I produced but that is usually how it is with my writing but after several days of working on this, it's what I've got. I hope I was able to accurately portray what the Doctor was feeling inside at the end of both Doomsday and Journey's End. It's definitely what I think he felt but your mileage may vary. Reviews are encouraged.