He sneaks into River's cell at night and takes her across the universe. Neither of them need as much sleep as humans, and he doesn't want to fiddle with the TARDIS controls all night; much as he loves his Sexy, it's only something he can do for so long. So he limits River's sentence to her days at Storm Cage and her nights are his. But there's another reason for his visits.
When the TARDIS is quiet, he remembers everyone he's lost. He's left alone in the shadows of his thoughts; thoughts that seize him like ravenous wolves in winter.