so one of the most intimate moments of BS to me is “Where are you?”
asking that question imply a sense of awareness about the other person - an almost psychic connection (which they developed later), an ability to feel the other’s presence and recognize they’re ‘not there’

even then john can read james so easily - can sense him, can feel him. that’s such a deeper connection than john has ever had. when did this happen? in the aftermath of the amputation, when he spent hours laying in flint’s quarters and got used to the different silences?

the silence of flint as he plotted courses; the silence of flint as he read; the silence of flint after a raid; the silence of flint at night before he fell asleep. silence has a sound. there’s a silence that fills up a room, makes you so aware of another person in it with you.

but there’s another silence, where if you close your eyes you can’t feel that other person. they’re not in that room with you. they’re elsewhere, they've transported themselves somewhere else.
john is well-versed in flint’s silences.
“where are you?” who are you thinking about?

who, in the middle of this terrible situation, is important enough to take you away from here?
its such a tender and caring question, with a request to come back from wherever he’s wandered off to. where are you? come back; there’s nothing there for you; i’m here, be here with me