That is the plan so far. John intends to do what he can for Sherlock, and if that means saving him, protecting him, healing his stupid cuts for the sake of experiments... He'll do all of that, no problem, no questions asked until it's all over.

He's known Sherlock for just over a week but he's already certain of that.

"First mate or captain, then. Close enough, either way."

Either way, they'll be right at each other's side, and that feels right, that's what really matters.