* CrowningMomentOfFunny: The crews differing reactions to The Doctor's Psychic Paper.
** Jayne sees "Doctor John Smith, monkey keeper".
** Kaylee sees "[[KnightInShiningArmor Sir John Smith, Director of Antiquities]]".
** For Mal? "John Smith, [[ArsonMurderAndJaywalking Accounting]]".
** The TARDIS takes a liking to Zoe, guiding her to a bathroom when she needs it, letting her inside Rose's room, [[TearJerker and showing her an image of Wash]].
** During the climax, when in some kind of ethereal realm that looks like Mal's old room on Shadow, The Doctor shows Mal a reflection of himself. Mal sees himself shining brightly, and notes that he and The Doctor, are the same.
* [[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.