** Starman Ghost himself states ''Not Alone'' was written to set right perceived issues with certain other TCB stories. Whether or not certain story plot points are established by fiat, have or lack substance and make sense are things that have divided the readership.
** Starman Ghost's own decision to delete the story from Fimfiction.
* HoYay: Between [[spoiler:Andrew and Ice Breaker]].
* MisaimedFandom: Readers who defend the humans putting ponies into [[UsefulNotes/WorldWarII internment camps]]. [[WordOfGod The author has said]] in comments that they're supposed to be an unjustified, kneejerk reaction motivated by racism and paranoia.
** Fans who want to see Equestria [[NukeEm glassed.]] [[spoiler: They don't get their wish.]]
** Also, fans who want to see all of humanity ponified and brought under the control of the Equestrian Diarchy. [[spoiler:They ''really'' don't get their wish.]]
** And the readers that don't seem to quite understand the fact that the story is a DeconstructionFic that runs on GreyAndGreyMorality.
* PatrickStewartSpeech: Arguably, the entire story is one of these to the original. Possible examples include the EFH posters and the [[spoiler: declaration of war speech]].
* TearJerker: The entirety of the chapter titled "He's Dead." Aside from being a tearjerker, it also outlines the exact FridgeHorror issue of the personality changes that come from the ponification.
** Andrew [[spoiler:is forced to lie to Thunderhead to make amends. It's the first time Thunderhead's been happy since his "birth," and it's not even true]].
* TheWoobie: Poor, poor Thunderhead. Imagine if you came into being at someone else's death.
** Andrew/Iceman as well. He's lost his best friend only to have him replaced with a crude caricature.
** The ponies involved with the EFH as of "The Longest Day". [[spoiler: After Bon-Bon outs them, it's decided that they have to leave Ponyville]].
*** Of note are Cheerilee, who [[spoiler: is no longer trusted to teach the town's foals]], and Mayor Mare, [[spoiler: who is removed from office]].