He knew. As soon as Jenny had gone, intrinsically, the Doctor knew Jenny no longer occupied the same universe. Back to being dead, so far as he knew, he could only sit on a bad he never used and ruminate the experience of meeting her in the first place. It had been a lot at the time, given the Doctor had tried so hard to block out anything Gallifrey-related. He didn't know then what he was gifted, so to speak, with knowing now--that his people hadn't been locked away in time for good.
Lamenting the loss of his daughter only dredged up more, the family he'd lost, the home he'd essentially abandoned in favor of traversing all of time and space. Even with the memory of a Gallifrey saved, trapped in a far less traumatic instance of time, he couldn't find the energy in him to be excited about the latest shift in unexpected scenery. Fat lot of good he'd been to everyone anyway. Quietly inspecting every nook and cranny, avoiding people at all cost, never making connections if he could help it, and certainly not trying to do more for Rose than what he'd already attempted.
Oh, but how he'd missed his Bad Wolf Girl.
He sat at the edge of his bed, hands between his legs and shoulders slumped as if deep in thought. Some might mistake him for sleeping, though the Doctor didn't tend to do that (let alone get caught doing so) short of when he was post-regeneration. He heard the door open, but failed to move until it registered that Rose was talking to him. Rubbing his tired features, a smile was immediately put on display as he turned to regard her as though he hadn't the foggiest idea as to why she was paying him a visit.
"Oh? What's gone on now, pirate ship? Kraken? The Lost polar bear? I've got more guesses up my sleeve if you like," and he knew instinctively what she wanted to discuss, yet avoided it anyway.