Disclaimer: I don't own Doctor Who no matter how much I pray to Santa :)
For him, the dream had been a nightmare forcing him to confront the truth. He is the doctor and one day his Amelia Pond, the sassy smart Scottish girl who'd been his very first constant in this new life, would have to leave. Just like all the others. She would outgrow him soon enough and then they would part, because he was the Doctor and that was how this worked.
The dark side of him knew this, in all probability it wasn't really dark at all, just negative. It was the tiny, niggling voice of reason in the back of his mind that whispered all the truths he tried to ignore. The part of him that knew what had to happen, what would happen and why. The part that knew Amy had to grow up one day because she couldn t run forever. The voice that whispered, no matter the delight he felt at pretending otherwise, that she was always going to pick Rory. The suppressed knowledge that there was no way in all of time or space that she would truly be happy to stay exactly as she is, right now, forever.
The moment the doctor understood what was really happening he stopped fighting, because the darkness knew this was how it had to go. Amy choosing him would hurt her and choosing Rory was the wise choice because when all was said and done, Rory didn't have to be a hero and Rory would always be there when he couldn't. He took some comfort in that thought, even though he would really prefer that Amy choose him.
Even though the doctor knew what the dark side of himself was doing, even if this was the logical and natural progression of events, it still hurt. He was only on his 10th regeneration, his 11th life. It would be a while longer before he could let himself be selfish with someone as frigile as a human.
Author's note: I'm assuming 1st Doctor is the first although I've heard somewhere he might not be. If I have time before next week I may add an Amy story.