Amy and the Doctor were in the control room and Rory was off exploring the TARDIS. Amy was reading while the Doctor piloted them off to only he knew where. He looked around and noticed the flower vases filled with roses set on various stairs around the room.
"Amy?"
She continued to look down at her book but answered back, "Yeah?"
"Where did all these flowers come from?" he asked as he moved towards the closest vase.
"Well I thought the TARDIS could use a feminine touch, I picked them up the last time we stopped on Earth."
The Doctor delicately touched the petals of one of the flowers and thought to himself, 'Of course they're roses, I just can't seem to escape her' and sighed aloud.
Amy finally looked up and saw the Doctor a bit misty eyed bending over a flower. "Doctor?"
He refused to look at her. "I once had a companion named Rose. She was the most human human, well except for the one time. She was all pink and yellow and I was brown and blue. She stayed with me through two regenerations. You would have liked her, you both seem to enjoy doing what I tell you not to do." he said and chuckled sadly.
"What happened to her, Doctor?" she asked quietly.
"We were forced apart; she was trapped in a parallel world. Of course my metacrisis is with her but still..." he trailed off. He still hadn't looked away from the rose.
Amy didn't bother asking what a metacrisis was and instead studied what she could see of the Doctor. "Did you love her?"
"I can't answer that, Pond." He swiped at his eyes, adjusted his bowtie, and spun around as if nothing had happened. "Now, we were off to the planet of the Tanyans! Did you know they have tusks?" And off he went on one of his typical explanations.
He never mentioned Rose again, but Amy never forgot that moment in the control room.
When they met River again, Amy asked her about Rose and at first all River did was stare.
"He actually talked about her?" she gasped, looking rather shocked.
"Yes, why?"
"Well he never talks about her. In all my time with him he's only talked of her a handful of times."
"Did he love her? I don't mean as a friend, but really love her?"
"I believe he did, though he'll never admit it to anybody except her."