Amy always said exactly what she meant. Therefore, when she'd said that she remembered, she did just that – she remembered everything, including the Doctor's little stunt whereby he had sacrificed himself to the cracks in time. Needless to say, she was not pleased, no matter the circumstances in which he had acted. Now, alone at last, she intended to make her sentiments fully known.
"Doctor," she said sweetly.
"Yes, Pond – what is it?" he replied, fiddling with the controls of the TARDIS and not paying her much attention.
"Look at me?" she asked.
The moment he did, her palm connected with his cheek, leaving behind a bright red handprint. Clutching at his face dramatically, the Doctor cried, "What was that for?"
"That was for sacrificing yourself like the noble idiot that you are," she declared self-righteously. "And this …" she advanced on him, the Doctor making no move to retreat. Feeling deserving of her wrath, he prepared himself to take his punishment like a man. Slapping him again, this time across his other cheek, Amy continued, "That's for leaving me alone again." Her indignation having been spent, she collapsed into the Doctor's waiting arms, sobbing uncontrollably into his chest.
"There, there, Amy," he said, patting her back reassuringly. "Everything turned out alright in the end, didn't it?"
"But you had no way of knowing," she countered. "You couldn't have been sure when I would remember, if I remembered at all."
"That was a chance I was willing to take," said the Doctor calmly. "It would have all been worth it as long as you were happy," he told her. "You got your family out of all of this, and that's what matters."
"But I didn't have you … my Raggedy Doctor," she said, smiling sadly up at him even as the tears continued to stream down her face. Acting on instinct, the Doctor raised his hands to wipe them away with the pads of his thumbs. His own pain forgotten in the face of hers, he cupped her cheeks with such tenderness and devotion as to leave them both breathless with anticipation.
"Amelia Pond, I'm going to tell you something that I probably shouldn't, but that you deserve to know. I'm going to tell this to you once, and then we'll both forget," he whispered. "Amy, I love you, and that's why I was willing to sacrifice myself. It was for you … everything. It always has been, and it always will be."
"Doctor …" she gasped.
Slowly, the Doctor lowered his head until their lips were mere millimeters apart. Then, they were kissing. Just once, but that was all it took to show them what could have been, and now would never be.
Forcing themselves to pull away, Doctor and companion nevertheless remained close, foreheads pressed together. "I love you too, Doctor," Amy whispered.
The Doctor smiled down at her, an age-old pain in his eyes as he knew what must be done. "My feelings for you will never change," he promised, slowly raising his hands to touch her head. Only needing the tips of his fingers to be in contact, he withdrew the memories of what had just happened from her mind. She could never know – she was a married woman. He would always remember, though – it would be his burden to bear alone, as had been so many things before.