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"Amelia." The Doctor's eyes shone with tears as he watched the little girl running around his TARDIS. Standing in the other side of the room, Clara frowned. The Doctor ignored her, completely absorbed in the sight in front of him.
As Amy walked towards him, she suddenly changed. No longer was she the child he met after he crash-landed on Earth after regenerating – she was now the grown Amy Pond he'd met when he returned for her. He couldn't quite see the difference, not the way humans referred to "seeing", but he could feel the difference in her as she walked down the stairs towards him, slowly turning into the woman he lost to the Weeping Angels.
"My Raggedy Doctor," She said quietly, a soft smile playing on her lips. Her hands gently cupped his cheek. "You were one of the two best men I've ever known. You always will be."
"I'm not a good man." His voice was somewhat hoarse. "I never was."
"You saved Gallifrey, didn't you?" He nodded. "You saved me and Rory. You tried to save River. You went out for a war just to do that."
"Good men don't start wards. Good men don't hurt innocent people." He was haunted by each and every one of his mistakes, even those that happened long ago. Even though he now knew for certain that he managed to save Gallifrey, the fact that he once destroyed his home and his people never once stopped bothering him. "Good men aren't dangerous for the universe."
"The Pandorica was opened by your enemies," She reminded him. "The Daleks, the Sontarns, the Cybermen – all the races set on destroying everyone but themselves. Their attempt to lock you down was only meant to allow them to destroy the universe. In the end, you used it to save me.
"Think about it, Doctor. If the good men would never have started wars, nobody would. Who else would've fought the destroyers? Who else would've stopped the destruction they can cause? If there weren't good men with the power to help the innocent, men who keep to their morality, to their rules, how would any race have survived?"
Looking into her eyes, the Doctor said what he'd told Madame Kovarian so long ago. "Good men don't need rules."
"On the contrary, my Doctor." Amy's smile was soft. "Only good men need and have rules. Their rules are what make them good men. Every man has his own temptations; his own desires; his own instincts. Some people's desires are destructive to others. The ones who harm the very same people you are trying to save are the ones who simply follow these desires – whether they've been programmed into them," She added when he opened his mouth to argue, "Or not. The good men are the ones who set their rules and follow them. If anything, that only proves that you are the good men that so many people in the universe see in you."
Seeing the agony in his eyes, Amy once again cupped his cheek. "You and the TARDIS are symbols of hope, of morality, of a better future. Not once have you broken those rules you set up when you first became the Doctor. Even when you harmed the very ones you intended to save, you were only trying to save others. You are the Doctor, and the Doctor always was and always will be a good man."
"You were the first face my new face saw." The Doctor's voice was quiet; his eyes filled with gratitude.
Amy smiled. "You were my Raggedy Man."
The Doctor returned her a smile. "Thank you, Amelia Pond."
"Goodbye, Raggedy Doctor," she said quietly as he hugged her, even though he knew she wasn't really there. She wrapped her arms around his neck, returning the hug.
"Goodbye, Amy Pond."
And just like that, she disappeared from between his arms. The Doctor turned to face Clara, happiness shining in his eyes.
"We all change, when you think about it. We're all different people, all through our lives. And that's okay, that's good, you've got to keep moving, so long as you remember all the people you used to be.
"I will not forget one line of this. Not one day. I swear. I will always remember when the Doctor was me."
He smiled as the Eleventh Doctor for the last time, his heart lighter, before regenerating.