It was well into the night, around two in the morning, and Walt couldn't sleep. He sat on the small couch in his apartment, watching a television that wasn't turned on. He had spent much of his time worrying nowadays: for his family, for his business, for his own life. Now, he worried more than ever. His last move, the murder of an innocent man to save his life and his job, had proven to be his most daring endeavor.
While staring blankly into the empty air, he thought of Jesse. Just a few days earlier, he had instructed Jesse to carry out a plan that the kid had previously advised Walt not to carry out himself. It was the hardest thing to do, forcing Jesse to kill when it wasn't in his nature. Walt wondered whether Jesse was straight-faced or emotional when he held the gun to Gale. Were his hands shaky and weak, or was he so hardened at this point that a steady hand and a quick pull of the trigger meant nothing? Walt didn't know which would be more heartbreaking. He knew he had somehow broken Jesse, and, at that moment, he wished only to apologize.
The boy would've never amounted to much; that much was clear. Jesse was a good kid, but he was also the sort of kid that no one gave a chance. He seemed unable to escape the path that society had laid out for him. His actions screamed otherwise, but his intentions were nothing but good. Walt was his polar opposite: A respectable man who, underneath his mild-mannered exterior, was an ambitious and manipulative villain. He realized that this is why he could so easily ruin his young partner's life. No matter what he did, everyone believed that Walt was a good man: even Jesse.
Jesse trusted Walt too much than what was good for him. Maybe it was why they were in their current position, Walt thought. While he had distanced himself from his emotions, Walt knew that his partner was falling apart emotionally at that very moment (who knows where). He wanted to comfort him, but he knew that Jesse deserved to be left alone, if just for a little while.
With every fragment of the little humanity Walt had left, he wanted to do right by Jesse. His other half, Heisenberg, knew that the man was extraordinarily expendable. For god's sake, he was some punk-ass kid with nothing but a high school diploma and a chili-powder meth recipe to his name. Nevertheless, whatever was left of Walter White wanted Jesse to have the happy life that he deserved. Walt knew that the younger man couldn't handle all that he'd put him through; he could see the ghosts flickering in the kid's crystal blue eyes. Jesse was in over his head, ironically, far more so than Walt himself was. All he wanted for Jesse was an escape from the misfortune in which they were ensnared.
Nevertheless, Walter knew that he was going to keep his partner by his side through all of their future entanglements. Without Jesse, there was nothing to stop Heisenburg from taking over completely.