* [[spoiler: LikeYouWouldReallyDoIt: At the climax, there is a scene where a person has to die to bring Mal back to life, and the two options are The Doctor, and a brand-new alien race created specifically for this story. [[SarcasmMode Gee, I wonder which one dies...]] ]]
** In all fairness, the author was already aware of this trope, [[AllThereInTheManual as stated in their notes]]. They just couldn't pass up the chance for some lovely spiritual drama, and it really is wonderful.
* TheWoobie: The Doctor. This is between "The Runaway Bride" and "Smith and Jones". The angst is rather understated and all the more powerful for it.