* AlternateCharacterInterpretation: Dash's love of speed and flying is extrapolated into [[spoiler: crushing claustrophobia]].
* BlackHoleSue: Ye gods, the deer warp ''everything'' to be around them. Of course, as they are obviously designed after Tolkienian High Elves, this is a rather difficult trap to avoid.
** Still, they are actually the only part of the story considered to be bad by fans of the story.
* FridgeLogic: Going to the princesses Celestia and Luna for assistance is never brought up as an option, and it's especially glaring when intervention on their part could resolve the entire plot quickly and without incident. [[{{Doylist}} Granted, from a narrative standpoint]], it obviously would make for a much less exciting story; but this option is never addressed in-story, let alone given a justification for why it never comes up, or why it wouldn't work out. This glaring flaw is the story's one major shortcoming.
** This flaw is explained in the last few chapters: [[spoiler:Twilight refused to contact the Princesses because she thought that would look like she didn't have faith in her friends. Privately, Fluttershy fears that her judgement is being addled by the Horn Rot, and when she takes a turn for the worse, the only thing keeping them from ''immediately'' contacting Celestia is that Spike is out gathering herbs to help tend to her.]]
** In the Epilogue, [[spoiler:Princess Celestia ''finally'' learns why Twilight hasn't been writing to her, and is taken aback, even wishing that they ''had'' let her know so that she could at least ease Twilight's pain as best she could…]].
** Arguably, FridgeBrilliance. [[spoiler:If Twilight were in suspended animation while a cure brewed…she'd awaken to eventually learn that ''three of her friends died getting the Beneviolet to her'', since she wouldn't have been able to teleport them away from a pissed-off World Snake.]]
*** Not quite. The basic premise of the story is that Twilight will die before the horn rot cure can be made. The Beneviolet is a faster way to recover. So if Twilight was put in suspended animation, the horn rot cure could have been made naturally and eliminated the need for the Beneviolet.
* LesYay: Rarity and Rainbow Dash in a couple of spots. There's Rainbow sucking on Rarity's horn in her sleep, Rarity tickling Rainbow when they were bathing, and this, from after Dash finally got the plural of 'Pegasus' right:
-->Rarity stopped hard. Her eyes widened. And in spite of the dire circumstances, she smiled enormously, lunging at Dash. “Oh, Dash, you did it! You did it! Nopony even needed to correct you! Why- why- I could just kiss you!”
-->She wrapped her front hooves around Dash's neck. The sky-blue Pegasus was taken aback for a moment, then grinned slyly. “Well, if you want to…”
-->Rarity drew back, an uncertain look on her face. Then she made a little noise and planted a soft kiss on Dash's forehead. “Done. Now don't say I never did it.”
* HilariousInHindsight: This fanfic was remarkably prescient about plots that were used in official sources:
** In an obscure comic from a German magazine, most of Ponyville gets paralyzed. Rarity travels beyond Equestria's border to find a specific variety of barley to cure them, and she meets a kingdom of earth ponies there.
** In the season 4 episode "[[Recap/MyLittlePonyFriendshipIsMagicS4E11ThreesACrowd Three's a Crowd]]", Twilight and Princess Cadance travel to the very edge of Equestria to find a rare flower, which is the fastest cure for a sick friend. Upon picking the flower, they're attacked by a giant worm.
* NightmareFuel: Wait, did they actually defeat that [[spoiler: World Snake?]]
** Answer to the original question: [[spoiler: No, the World Snake was later killed in the true sequel by the [[EldritchAbomination evil immortal deer]]. In one shot.]]
** When [[spoiler:Falalauria says she should kill Rarity and her friends]]. It came so suddenly.
** At first, the sudden ArtShift of the text when [[spoiler: Rainbow Dash enters the Dreaming]] can be somewhat freaky, especially considering the actual scene. It wears off after a minute, but still.