The following takes place between "The Long Game" and "Father's Day".
I do not own Doctor Who.
As soon as that lying, stupid ape, Adam, was left at home, Rose disappeared. This unnerved the Doctor. That girl was always under foot when he wanted to be alone, and now that he needed her, she was nowhere to be found. Perhaps she was more attached to Adam than she'd let on and was along in her room. He went to her room, though, and she wasn't there.
"Where is she, Old Girl?" He queried his magnificent ship.
But the TARDIS wasn't telling him.
Fantastic. That could only mean one thing: Rose didn't want to be found. Suddenly, it all made sense. Rose had seen a glimpse of the Oncoming Storm when he faced that Dalek in van Statten's museum. She was terrified of him, and now she had run away. Sure, she had seemed fine on Satellite 5, but stupid Adam was there. Perhaps she thought the boy could protect her? Now he was gone, and Rose had run for her life. And why shouldn't she? She finally saw him for who he really was: a killer. Not only that, but he had committed genocide. And the girl was smart enough to put two and two together and realize that if he killed all the Daleks, he likely also killed his own people. No, the Doctor didn't blame her for hiding from him.
He began searching the TARDIS, angrily slamming open every door he came across, looking for her. He wasn't angry at her; he was angry at himself. He had shown his true colors, and now he was about to lose the best thing that had ever happened to him! He had to find her so he could take her home! So this is how it would be now. No one wants to travel with a killer! He took out his frustrations on the walls and doors of his ship, pounding his fists and yelling. Luckily, she was patient and didn't hold it against him. She just hummed and tried to assure him that everything would be ok.
Finally, after hours of searching, and walking past the same doors over and over due to the TARDIS rearranging the corridors, the Doctor came across a door that he had never seen before. With gentle prodding from the TARDIS, he knew that Rose was inside. He threw it open, ready to tell at her, but what he saw took the words out oh his mouth.
Before him was a beautiful sight. The room was huge and devoid of anything but candles: millions and millions of candles of every shape, size, and color filed every inch of the cavernous room. Not all of them were lit, but enough were that the room was filled with a soft, warm glow. And there, kneeling at the end of the front row, lighting a candle that looked decidedly like a miniature TARDIS, was Rose Tyler.
"What's all this?" He asked dumbfoundedly.
"This is for you. Sorry that I disappeared soon after we came on board, and I'm sorry that the Old Girl sent you on a wild goose chase through her corridors, but we wanted this to be a surprise. This was my idea, but she helped. She had to, because there was no way that I could do this on my own."
"It's beautiful, but what is it?"
"This" Rose gestured broadly around the room. "Is your life. Every candle in the room, whether lit or unlit, represents one life that you have touched in your 900 years of time and space, either directly or indirectly."
"Blimey! I didn't realize that there were so many!"
"The TARDIS has been keeping track."
"I can see! But why aren't all of the candles lit?"
Rose grew silent for a moment. Then she said softly, "Those candles represent lives that were lost because of you."
Of course they do. Suddenly, the Doctor no longer saw the brightness of the candles that were lit, but the darkness hovering over those that were not. There were so many! He wondered how many of them represented his own people on Gallifrey.
Rose noticed him tense and decided to direct his attention back to where it belonged. "But look at the candles that are lit, Doctor! Those represent the lives you have saved!"
He saw what she was getting at. There did seem to be more lit than not, but he still could only see the lights that were out, the lives he had ended.
Again, Rose seemed to sense what he was thinking. "Old Girl, show him what would have happened if the Time War had not ended the way it did."
Suddenly, most of the candles were extinguished. The room, which had been full of a warm, inviting glow only seconds before, was now cold and mostly dark. There were a few candles that were still lit, but they were so few and far between that their light did nothing to brighten the room. They were the candles that were previously unlit.
"Look, Doctor. See how many lives you've saved?" The room returned to its original splendor as the room once again was filled with the light of the millions of people who were saved that day.
"Yes, Doctor, you've killed. Yes, you've killed your own people. But you, Doctor, are not an evil man. You have lost your planet, but saved the universe!" She leant over and picked up a pink and yellow candle from the front row. It was one of the candles that was extinguished when the room was dark. "And on behalf of the millions of us that you saved that horrible day, I thank you, for doing what needed to be done, and I'm sorry that it happened the way it did."
The Doctor opened his mouth to speak, but a moan escaped his lips instead as he collapsed to his knees and wept like he had never wept before. Rose knelt next to him and wrapped both arms around him in a giant bear hug as he sobbed uncontrollably into her shoulder. Her shirt was getting soaked, but she didn't care. After awhile, he calmed down, but still clung to her like she was his lifeline.
"Thank you," he whispered. "Thank you both."
"You're welcome," she replied. The Old Girl hummed her agreement.