“Wait for me.”
The Doctor slipping these three words into Bill’s subconscious when thinking she’s still alive to hear them was, to me, an equivalent to three other words he used a lot with Clara: “Duty of care.” He said he couldn’t promise keeping her from getting killed, but like all companions, he does try to restore damage that seems reversible.
These scenes were both haunting and comforting with the latter only due to the fact that it was the Doctor calling out to her. For the record, I have a huge fear of a figure standing over one’s bed, but because it was the Doctor, I was fine in that scene. It was Mr. Razor who made me jolt instead, and for good reason when it was revealed who he was later on! XD