I wanted the sudden "reveal" that Bones is actually alive to be so understated that the understatement itself is almost a shock. I wanted to shake readers with the knowledge that Jim has known the whole time, and he's not mourning Bones' death, but trying to recover from the shock of how close he almost came to dying.

And... really? You couldn't handle Jim/Bones as a ship? Then I shall proudly take credit for spoiling that for you. :D