* AlternateCharacterInterpretation: Littlepip as a VillainProtagonist. Several of her actions can be seen as morally questionable as she can be pretty ruthless towards her enemies. The story itself even acknowledges this viewpoint, with Red Eye explaining how they are NotSoDifferent. A few fans may consider this a BaseBreaker.
** In turn, Velvet Remedy (while she may have good intentions) can be seen as [[BlackAndWhiteInsanity self-righteous]] [[SmallNameBigEgo egotistical]] [[BitchInSheepsClothing bitch]], who mocks and insults Littlepip and her other companions for no good reason. Even after her CharacterDevelopment, she is shown to still have traces of this
* ArcadianInterlude: The sudden pornographic scene in chapter 20.5 (a "deleted scene" chapter by another writer which is treated as potentially canon by the original author).
* AwesomeMusic: A fan performed [[http://www.youtube.com/watch?v=ksn91wXHgx8 this piece]] in honor of Littlepip, the first in what will be a line of several FO:E inspired songs. The instrumentals and vocals are excellent, and the lyrics fit Littlepip's struggles throughout the story perfectly.
-->''I'm sick and tired, of all this fighting. Not sure if this blood is mine...''
** A good number of brony musical artists have composed songs inspired by ''Fallout: Equestria'', including dozens of songs available on YouTube and even music featured on the "Balloon Party" album series.
* BaseBreaker: [=LittlePip=] and Velvet Remedy, as seen in AlternateCharacterInterpretations up above.
* DarknessInducedAudienceApathy: The dark setting and questionable morality of the protagonists make the story rather hard to read for some people.
** [[spoiler: The Memory Orb sequences are so bleak, depressing, and hopeless that you eventually get ''used'' to seeing the main cast of ''Friendship is Magic'' dying horrible, pointless deaths.]]
*** [[spoiler:Not just the main cast. In Canterlot, a pony (who while never identified is often assumed by fans to have been [[EnsembleDarkhorse Lyra]]) [[ImMelting died horribly]] from [[DeadlyGas Pink Cloud exposure]].]]
* DesignatedHero: Arguably Littlepip. [[BlackAndGreyMorality It may or may not be intentional]].
* FridgeLogic: A fair bit.
** [[spoiler:The Celestia One megaspell can only reach areas where the cloud cover breaks, and the sun can shine. The Enclave's most powerful forces generally make a point of staying *above* the clouds anyway.]]
* HarsherInHindsight: [[spoiler: So you'd like to be a tree, eh, Fluttershy?]]
** The story depicts Ditzy Doo as unable to talk because her tongue was cut out. Later, the referring to the character in the show as Derpy, combined with her voice, lead to backlash from MoralGuardians for the UnfortunateImplications, resulting in her voice being changed and likely making it so she won't be getting another voiced part anytime soon.
** Friendship is Magic's [[Recap/MyLittlePonyFriendshipIsMagicS2E25ACanterlotWeddingPart1 second season finale]] includes several elements that are eerily similar to FO:E, such as [[spoiler: Canterlot enclosed in a [[DeflectorShields magical shield]] and a legion of corrupted WingedUnicorn SlaveMooks led by an obnoxious LargeHam HiveQueen, who was voiced by [[Creator/KathleenBarr the same actress as Trixie]] with an added [[VoiceoftheLegion reverb effect.]]]]
* HilariousInHindsight: Watcher is a mysterious gravelly-voiced nigh-omniscient observer who communicates by hijacking floating robots - just like Ulysses in [[VideoGame/FalloutNewVegas Lonesome Road]], which was released several months after ''Fallout: Equestria'' started.
** Littlepip thinks the name "Pipsqueak" would be ridiculous. Then an actual character named Pipsqueak appeared in the show.
*** And what nickname did Zecora give him? Little Pip!
** All of the magic spells that Kkat came up with before season 2 even started, including memory transfers, bypass spells, and self levitation.
** Now add in the harnesses used to hold the lances for Crystal Ponies while jousting, which resemble very early battle saddles.
** [[DrunkontheDarkSide Corrupted]] by an enhanced source of magic, [[spoiler: Trixie]] sets herself up as a tyrant. [[Recap/MyLittlePonyFriendshipIsMagicS3E5MagicDuel Sound familiar?]]
** Also from ''Lonesome Road'', the [[http://fallout.wikia.com/wiki/Shoulder_mounted_machine_gun SMMG]] and [[http://fallout.wikia.com/wiki/Red_Glare Red Glare]] look like battle saddles retrofitted for human use.
** And now Twilight gets [[Recap/MyLittlePonyFriendshipIsMagicS3E13MagicalMysteryCure involuntarily transformed into an alicorn.]]
** Zecora crafts a potion that gives zebras bat-like wings. Two months later, the episode "Luna Eclipsed" introduces bat-winged ponies.
** Why did the Everfree Forest mutate into a much more horrible and deadly place when it was never hit by a megaspell? Because the Elements of Harmony were removed, and their presence in the Forest had been holding the horrors back... much like the revelation in the Season 4 premiere.
** ''Inspiration Manifestation'' confirms dragon tactic of "eat it" for disposing of hazardous magical items.
** ''Twilight's Kingdom'' shows extremely destructive spells similar to balefire bombs, complete with mushroom clouds.
** In the chapter ''The Moral of the Story'', Pinkie Bell makes the remark that "Pinkie Pie’s only regret was that she couldn’t be everywhere helping all the troops all the time!" ''Too Many Pinkie Pies'' takes on an almost eerily similar premise.
* HypeAversion[=/=]HypeBacklash: This is ''easily'' one of the most famous ''Friendship is Magic'' fanfics out there. It has fan art, fan music, there are fan games being made for it including ''Fallout 3'' mods, and it has inspired dozens of spin-off fics. Does it deserve all this attention? Not everypony would agree.
* IdiotBall:
** Littlepip converses with Watcher while she's wearing raider armor - the only thing she could find at the time - and Watcher fails to warn her about the negative connotations which later lead to a near-fatal misunderstanding.
** The first alicorn [=LittlePip=] meets decides to stand perfectly still and hurl taunts while Pip puts everything she has into casting a powerful spell. [[WhyDontYouJustShootHim Naturally, that spell kills her]].
** In the Balloon Orb, [[spoiler:Pinkie Pie's refusal to [[ItMakesSenseInContext inform herself as Pinkamena through the soul mirror]] of the oncoming apocalypse when LP tries to warn Pinkamena through her, stating that the knowledge is a secret despite this event prompting real world Pinkie Pie to create and plant the mane six memory orbs for LP to find later in order to fix the world. Depending on how one takes this, it could actually be [[FridgeLogic Fridge Logic]] as Pinkie Pie's future reading abilities may have shown her no other clean outcome possible ''except'' to let the world melt and have LP clean up after.]]
*** Which now makes sense, due it being made clear that Equestria time travel runs on the StableTimeLoop. Nothing could be changed about the past.
** In his planning, Red Eye [[spoiler: somehow ''forgets'' one way [=LittlePip=] might use her signature ability - extremely powerful telekinesis - which leads to his humiliating defeat during the final confrontation between them]]. He immediately [[LampshadeHanging lampshades]] the moment.
* InternetBackdraft: Quite a bit, mainly due to combining MLP with something as dark as ''Fallout'', as well as the seemingly meanspirited way [[spoiler:the Mane Six and their friends met their ends]].
* IronWoobie: Ditzy Doo. When the megaspells dropped, she was caught at the edge of one, which turned her into a Ghoul. She's spent the next 200 years doing whatever she can to survive, with the always present possibility that her mind will degrade to the point where she becomes little more than a mindless beast. This also has the effect of making surviving ponies [[FantasticRacism reluctant to go near her]], since nopony wants to be around when a zombie flips out. But even with all this, she is still friendly and helpful, to the point where Littlepip calls her the nicest pony she's met in the wasteland[[spoiler:, and later becomes the new Element of Laughter.]]
* MagnificentBastard: Red Eye.
* MoralEventHorizon: A number of ponies in the story cross this. Among them:
** [[spoiler:The Steel Rangers invading Stable Two and attempting to slaughter everypony in it just to get at the pre-war technology it holds.]]
** [[spoiler:The Enclave attempting to destroy Friendship City just to kill one Dashite (prior to the attack commencing one of them even shoots a terrified filly who was trying to get away from Littlepip, then attempts to justify it by saying that they couldn't take any chances.)]]
** Littlepip treats her [[spoiler: massacre of everypony in Arbu as this.]]
* StrawmanHasAPoint: Red Eye's propaganda states that all races of pony are equally important. He seems to consider the opposition that earth ponies are the best, which seems laughable. His opposition's points seem to be better than his, and then you realize that [[spoiler:the pro-earth pony Stable he's from invented cybernetic implants and cured old age with only the tiny population of one Stable]].
* UglyCute: Ditzy as a ghoul, who despite looking and smelling like a body that's been in the sun for a few days, is one of the most friendly and genuinely helpful ponies in the story.
* TheWoobie: Get out yer hankie, it's easier to count the characters who aren't this trope.
* WhyDontYouJustShootHim: Antagonists frequently back Littlepip into a corner, and [[VillainBall wind up snatching defeat from the jaws of victory]]
** Those raiders in [[spoiler: Ponyville]] know where Littlepip is hiding for the night, and settle for leaving a landmine by the front door instead of shooting her while she's asleep.
** Instead of killing her, [[spoiler: Mr. Topaz]] engages Littlepip in conversation and [[spoiler: The alicorn in Appleoosa]] taunts her.
** [[spoiler: Littlepip is captured after attempting to escape Fillydelphia and killing a few guards. Red Eye insists she be sent to The Pit instead of executing her outright.]]
*** At least [[spoiler: Red Eye]] had a good excuse for not doing so. [[spoiler: He wanted her to survive so she could be part of a new Alicorn god.]]