Eagleland: Columbia, both in being a fairly obvious United States counterpart, and, well, being full of Griffins. Though oddly enough, writer's notes indicate the country actually called Eagleland is an England expy. It is also full of Griffins, and despite claims otherwise, neither the Doctor nor Running Gag are Queen there.
Earn Your Happy Ending: Perhaps the central Tenant of this fic. Life is hard, we will make mistakes. Bad things can arise from good intentions, and sometimes the best of loves can be lost to the whims of fate. However, if you own up to your mistakes, trust in each other, never give up and believe in The Power of Friendship, anyone can change, and reach exactly what they needed.
The Seven Dreams/Nightmares side stories tend to work towards this as well. While the Nightmares are dark, so far every member of the G2 mane cast has managed to have a relatively happy ending.
G2!BonBon manages to survive, raise her niece, and ultimately her journal becomes an Apocalyptic Log preserving aspects of Pony civilization, just as she intended.
Patch manages to recover all the Shards of the Rainbow of Light, overthrowing multiple Evil Overlords, starting a family and being Happily Married to Buddy, and ultimately reuniting with her Bright Glow.
Melody discovers that her hard work throughout her life essentially saved music and preserved it for the future, and her song "Sweet Music" continues to modern day along Rarity's family line.
Bright Eyes is probably the best example. After losing her memory in the explosion, she spends many years gradually regaining her memories. Once she does, she's forced to fight against Cruel Eyes/D___t to prevent him from reconstituting himself and threatening existence by consuming the infant concept within her. But she manages to destroy him, reignite her friendship with Moki, and lives the rest of her life successfully bringing back Earth Pony Magic and enjoying her time with her husband and their family. The last scene shows her and Lancer reenacting their first date in the afterlife, their journey complete.
This is essentially the point of the Dark World Series, to see if the Dark World Mane Cast can finally end Discord's tyranny. And they succeed. After a thousand years in Discord's World of Chaos, having to literally fight their friends to redeem them, Fluttershy and Pinkie Pie dying, having to defeat several deities and other dangerous enemies, and finally fight a Mad God leagues stronger than Discord to put an end to a several hundred million year old "Groundhog Day" Loop, the Bad Future is saved, all the Chaos Six (including Fluttercruel ultimately) are redeemed, Rarity (or rather Queen Libra) and Spike are Happily Married, and even Discord finds redemption.
The Shining Armor Arc ends like this as well. After going through hell to defeat Makarov and save the world, Shining has to fight for his existence against the Blank Wolf, managing to finally defeat it alongside Cadence and make his existence concrete, and proposes to Cadence. Meanwhile, Gag and Garnet are engaged and Minuette managed to destroy the Master once and for all, earning a life of her own in the process, and becomes an Official Couple with Captive Audience.
The Earth Prime Theory: "Applejack's Dream" establishes the existence of a "Heart World" from which the Pony POV Series world and all other Alternate Timelines diverged from and which anyone still connected to are effected by, implied to be the main series timeline. However, in an interesting twist, it is possible for a world to "break off" and continue on its own without any connection to the Heart World. The plot of that chapter involved preparing for the possibility that would happen so as to prevent Applejack from going insane and turning into Nightmare Mirror in the even that it did.
This bites Nightmare Eclipse in the flank when her plan has basically made her the Heart World Nightmare Eclipse, and tied all her other selves to her. Meaning defeating her defeats them all.
Subverted: While Fluttershy and Fluttercruel are forgiven, Princess Luna gives them a severe royal punishment for their misdeeds as a result. And not only do some ponies not forgive Fluttershy, she outright says she may never forgive herself.
Also brutally surverted with the Sunnytown Ponies, who, because they've not accepted responsibility for their murder of Ruby, are still cursed when Princess Gaia's spell is broken.
Played straight with the Dark World Mane Cast. After Twilight's, Applejack's and Rarity's Heel Face Turns, the Apple/Pie family accept them as allies and help them despite the fact that they spent 1000 years serving Discord and killing hundreds if not thousands of ponies, dragons, and changelings for him. Justified considering what Discord did to them, plus random transformations are regular occurrences in Dark World, so the explanation they were brainwashed into his Co-Dragons wouldn't garner as much scrutiny as it would before Discord. It should also be noted they already considered Applejack a saint due to her good deeds.
Discord is depicted as such in this story. Equestria was a peaceful place (implied to possibly be the G1 world) until he descended on it and began his reign of chaos and destruction. He's so chaotic that even the Truth can't comprehend him.
His parents, Havoc and Entrophy are even more this trope. Entropy's pupil absolutely dwarfs Celestia and she's a being that Celestia absolutely refuses to describe in detail to Twilight. Havoc, embodiment of mass hysteria, is described as every nightmare everypony ever had or ever will have whose voice would leave a mortal pony a horrified wreck. Entropy erasing Havoc from existence then him willing himself back into existence is their version of one member of a bickering couple shoving the other. Also, the Windigos are tiny fragments of Entropy.
Celestia and Luna's parents also qualify, though they're benevolent and won't drive ponies insane if seen in their true form, just really, really confuse them. Another trait about all four Elders is, according to Word of God, they're multiversal singularities, meaning, unlike their children, there's only one of each of them in the entire multiverse, the different versions are merely aspects of the same being.
Another example was during the Alicorn and Draconequi War, Entropy commanded all the Shadows of Existance in her realm to merge together into a monster named Legion. While we don't see much about it, we see what such a creature could look like thanks to another universe.
Nightmare Whisper, Princess Gaia's true form.
There's also Nightmare Mirror, Applejack's Alternate Self and potential Superpowered Evil Side. Not only is she massive, her appearance is constantly shifting and she's covered in eyes that force those who see them to face painful truths about themselves.
While he began as an Equineoid Abomination, by the time General Admiral Makarov reveals his true form, it's mutated into one of these: a gigantic vaguely Equine shaped mass of wailing shadows that seem to look at Shining that's features are constantly shifting with no pattern or reason to it with eyes made of an unearthly white light. The sight is so horrifying Shining Armor has a Freak Out both times he glimpses it. Think about everything that's happened to Shining and that's really saying something.
There's also the Shadows Who Make, Watch, and Rule, entities that the Alicorns and Draconequi allude to and which Celestia refuses to explain the true nature of to those in universe because they'd Go Mad from the Revelation. They're actually us.
Lilith, the First Witch and True Witch Queen is this. While she's humanoid, her powers, scope, and unsettling nature put her more into this trope. A being of so saturated with evil magic she's become made of the stuff, she could destroy the world and everyone in it if not stopped, leaving nothing but shadows that serve her, countless creatures turned to stone, and dust that used to be the ones she sucked the life out of. Thankfully, the G1 Cast defeated her, but she later returned as the Shadow Queen.
Eldritch Location: Discord's castle in the Dark World is implied to be this for most of the arc, and it's finally confirmed when the heroes try to use the Elements of Harmony on it (as an attempt to cut short their war with Discord), and it grows legs and runs away. Thing is, it seems to be as neutral as it is chaotic, since Applejack talks it into letting them get through to Discord by promising to not purify it (which would essentially kill it). Subverted after Queen Libra takes power, as she removes the Chaos, but keeps its sentience and ability to move.
Dark World in general probably qualifies, considering Discord made it a nonsensical hell hole where things are never the same two days in a row and apparently it raining water is considered a shocking event. Since Ponyville was the Chaos Capital, it had it worse.
The spirit world is essentially this as well. Time as we know it doesn't exist, Law of Conservation of Mass doesn't apply, and it's possible to exist in multiple places at once (no time travel involved).
Entropy's realm of Oblivion also qualifies, featuring a starless sky, floating blocks of ice every where, an ocean literally made of chaos, and is all an extension of Entropy Herself. It can be assumed the same applies for the other Elder's realms.
We see it later in more detail and discover that it also has locations from parts of time that no longer exist, only now empty and desolate. The Ocean of Chaos also seems to be inhabited by monsters of some sort.
Pandora's Realm. It's a nonsensical labyrinth with bookcases floating everywhere, stairways going every direction but the right way, and various fictional characters running all over the place.
The Rumours World of the final arc is this, with every type of rumor coming to life and everyone's history caught in knots.
Also the World Tower, which is the heart of the entire world, and filled with contrasting.
Elemental Absorption: Concepts can recharge their power by getting close to the thing they represent in action. This is shown by Rancor being immune to physical violence (she can only be harmed by things that don't count as violence or being tricked into hurting herself) and being able to recharge herself by going to Neighpon and absorbing the passion radiating from some kind of card game in progress. Dark World!Celestia and Luna have Rainbow Dash fly them into space so they can recharge directly from the sun to get back in the fight with Nightmare Eclipse/Paradox.
Eleventh Hour Superpower: Shining Armor gets special, stronger armor and a similarly strong riot shield from Pandora and unlocks his true power in 17.1-17.2, giving him a much needed boost to turn the tide against Makarov. Later the rest of Misfit Actual and Gilda get the armor as well.
Empathic Environment: After her Heel–Face Turn in the Dark World, Twilight awakens to find her room covered in plant life (the two potted plants that her parents were turned into by Discord having grown to cover the room), with birds singing and the ceiling broken away to let the sky appear overhead.
The Empire: The Hooviet Empire, an expansionist, deer-run Expy of the Soviet Union (with elements borrowed from Nineteen Eighty Four), which seem set up as the antagonists of Shining Armor's side story.
Empty Shell: The Shadows of Oblivion inhabiting Entropy's Realm are this, being little more than twisted shadows of the ponies they once were without their Lights of Existence. They also seem to crave to steal the places of others that still have existences.
End of an Age: The G2 world is shown as a Golden Age of Pony civilization, and we've so far seen two different perspectives — first Celestia's, and now the seven main characters of G2 — on how Destruction nuked it back to the Dark Ages to prevent the erased G3 world from coming to be again.
Enemy Mine: Twice in the Dark World, the Changelings were forced to side with Discord's forces against a bigger threat. Though the first time backfired on them, they apparently were smarter about it the second time.
Long ago, a group of extradimensional invaders attacked the pony verse. Their goal was to force all life into becoming their playthings and twisting reality into a never-ending hell. This was enough that Fauna Luster and Entropy agreed they needed stopped (stated to be the one time in all of creation They ever agreed on anything. Fauna Luster ordered four of Her children to defeat the invaders while Entropy ordered the Draconequi to stand guard and keep them from escaping.
While the heroes are unaware of it, or that Discord has even escaped, Discord and Nightmare Diamond seem to be helping them against Chrysalis, presumably because, as shown in Cadence's Bad Future vision, Discord would be in trouble as well should Chrysalis win.
An alternate version of Nightmare Mirror drops a piece of the Truth into Applebloom's eyes, saying it will aid in stopping Discord's plan in some fashion. What seems to be Nightmare Manacle also later helps Celestia restrain the twisted version of herself she becomes when Discord's plan effects her. Their dialog suggests they're doing this because they're on this side this time.
Enemy Within: Fluttercruel is a subversion, as not only does Fluttershy defeat her Badass Pacifist style, she becomes a valuable ally. Even when Fluttercruel gets out, all she wants to do is actually live for a change and not be stuck inside Fluttershy all the time. Played straight with Angry Pie from Pinkie Pie's story and Loneliness from Trixie's. Unlike the other two, Loneliness' creation is implied by Word of God to be something else besides a foreign entity introduced by Discord or a fractured piece of Trixie's personality.
Played straight again with a villain, Nightmare Whisper-her true form has a ruby containing a filly version of her that eggs on her Knight Templar qualities, and even turns on Fluttercruel when the latter gets a body of her own. It's later revealed that it's the repository of all the negative feelings Princess Gaia devoured, and a warped version of Flutterrage.
Cruel Eyes/D___t from Bright Eyes' Gaiden story. Since she was the mother of the G3 world, Bright Eyes' had an infant concept inside her, which D___t's Shadow of Existence wanted to take so he could exist again.
Enemy Without: An inversion for Fluttercruel and Nightmare Whisper, as Fluttercruel literally severs her connections to Nightmare Whisper and enters the battle to aid the heroes. What follows is an epic battle of wills between two Fluttershies: one that was good and corrupted into evil and one that was created evil and taught to be good.
Queen Chrysalis is this for Cadence, being her own cast off Shadow of Existence given life by Pandora.
Nightmare Eclipse/Paradox, as opposed to the other 'Super Nightmares' (Whisper and Mirror), she looks like a normal, if dark and menacing, Alicorn. However, the fact she's a several hundred million year old evil that's reset the timeline over and over again, along with her occasional habit of speaking with a Voice of the Legion when singing or pissed off, makes the normalcy just that much more disturbing.
To a degree, the Changelings may count, but they're far less alien than most. Professor Kabuto, however, has shades of this. Not only is he a powerful alchemist, he's altered his body with dangerous experiments and alchemy, including extra spider-like legs that can emerge from his back, Super Speed, No Sell tranquilizers, and a Healing Factor capable of regenerating from an arrow wound with ease on top of the typical Changeling traits. He can also go One-Winged Angel with a special potion (which he implies he intends to make permanent once it's perfected) which required altering his body just to be able to use it. Garnet almost throws up just thinking about how he managed to implant the legs and the number of Changelings he killed in the process. Hispersonality doesn't help make him feel any more equine.
Queen Chrysalis arguably counts, considering not only is she a Changeling, she's essentially the discarded, heavily burned and mangled corpse of Cadence's original body given life by Pandora, making her a fusion of Harmony and Chaos. Even by Changeling standards she's considered a mutant.
Energy Beings: Ball Lightning, moving masses of lightning born when lightning adheres itself to small bits of mana in the mana streams. They are unpredictable and seem to have a mind of their own, and seem enjoy fooling around with ponies. However, they can also be quite dangerous, and their antics range from just bashing ponies around a bit to blowing holes through airships as they do when Shining's group encountered them, which ultimately results in Ranger and Sunset's deaths. Thankfully, they're also shortlived and don't appear to be sapient.
Discord, obviously, but also Angry Pie, the personification of Pinkie Pie's supressed emotions at what discord put her through, and Loneliness.
In Pinkie Pie's Side Story, we discover he has a brother named Anarchy and their parents are Havoc (mass hysteria) and Entropy (heat death). Apparently theres seven siblings, but only him and Anarchy have appeared. Strangely, while he's far from a nice guy, Anarchy was actually trying to save the universe with the Alicorns. It's implied that Discord was off turning the Flutterponies into paraspritesFor the Evulz at the time.
Pinkie's "Butterflies" chapter reveals that he has a sister named Strife, who embodied conflict, natural selection, and competition. While not exactly a nice guy, she's far from evil and plays the Final Boss of the G3 timeline simply to give the survivors a chance to fight for their survival instead of fading away with no chance at all. We also see his brother Destruction, embodiment of disaster and well...destruction and Pandemonium, whom we don't really find out what she's the spirit of, though she says she's also known as Desire and prefers to be called Pandora, and inspires artist but can't understand why she tends to drive artists insane.
Epic Fail: Any time Shining Armor tries to shoot something due to him being an absolutely horrible shot.
Apparently, Ellis and a friend of his actually Shining himself tried to make a cider still for one of their superiors once. They ended up making a mass driver by accident.
Fluttercruel finds herself being judged by a Jury of the Damned, who sentences her to lose her sapience. She realizes Fluttershy still needs her help to be saved from the darkness and refuses to fade away until she's made amends for causing her fallin the first place. She has to fight her way out of the court, getting clawed up pretty bad in the process, to make it back to the world of the living to make her Big Damn Heroes moment and help the Mane Cast save Fluttershy from herself.
Dark World!Applejack has to fight her way out of Oblivion during her redemption
Dark World!Fluttercruel has to fight off a Thestral that tried to escort her to Hell, feeding it it's own wings, then possessing Sparkler. Since Chaos Verse!Fluttercruel also ended up having to escape Oblivion (with her father Discord's help), this means every known Fluttercruel has done this at least once.
Dark World!Discord and Fluttercruel genuinely love each other, to such a point that they grieve when one thinks the other is dead or dying and Fluttercruel has a complete breakdown when Discord is mortally wounded by Rancor. According to Nightmare Eclipse/Paradox, she's the only reason he even tries to beat her anymore.
Discord also begs the Dark World!Mane Six not to hurt Screwball and Mad Tiara/Diamond Tiara, who are his nieces. He even sends the two of them away with specific orders to never try to fight the mane six for his death because they'd not stand a chance and likely die.
Despite all the evil, horrible things they've done, Nightmare Paradox and her Psycho Rangers seem to genuinely love each other as friends, to the point they can still use the Elements of Harmony. Paradox has even been looking for a Nightmare Rarity because of what it'd mean to Banneret. Nightmare Banneret and Mirror also still care for Rarity and Apple Pie as well, but not enough to spare them (though its implied Mirror may have spared her Apple Pie in some way).
Digger Wasp, one of Chrysalis' Co-Dragons, seems to genuinely love and worry about his sister Jewel Wasp to the point of arranging for her to be kept away from the invasion out of fear of her getting hurt.
Chrysalis developed Lima Syndrome for Sweetie Belle to the point of blowing her masquerade to try and reclaim her. Unfortunately, when Sweetie sends a letter requesting she turn good and stop the invasion, this love isn't enough to stop her. However, Chrysalis still seems to be effected when Sweetie Belle is mentioned.
Everyone Has Standards: Despite running on Blue and Orange Morality, the Draconequi still have things they consider horrible. All of them hated the idea of the Windigos winning to the point it's one of the few things they seemed unanimously agreed on. Anarchy is not happy with Discord's Evil Overlord tendencies (an immortal king with an unending reign of tyranny does not sit well with the Spirit of Revolution and Freedom) and Strife sincerely considers every being has a right to fight for its survival. Even by their standards, Havoc's Avatar went insane and D___t was a Well-Intentioned Extremist.
Out of all the Draconequi, Rancor is the only one who doesn't hate Nightmare Eclipse for one reason or another. Entropy is unclear, just that she's slightly less apathetic.
Even the other Changelings consider Kabuto, Chrysalis' resident Mad Scientist, to be sick, twisted bastard. According to Digger Wasp, half the swarm is afraid of him, while the other half want to kill him.
Zombies are apparently extremely common in Dark World (though not Zombie Apocalypse common) to the point they're treated like any other dangerous animal.
Everything Trying to Kill You: Dark World tends to be like this, considering its a World of Chaos were Pony-Eating Rocks are common. That said, the ponies adapted and now blowing up monsters is considered a household choir.
Said almost word for word by Twilight in regards to Discord, siting how their victory was only possible because of this trope.
Luna's sidestory reveals it was Nightmare Moon who cursed Sunny Town for killing Ruby. She thought Ruby would be thankful for her doing this and tells her she can either pass on or join her. Ruby chooses to stay in Sunny Town and try and help break the curse. Nightmare Moon is completely shocked that Ruby could forgive those who murdered her and try to help them find their redemption.
Nightmare Eclipse/Paradox is incapable of believing Discord could actually have good in him. She also is at a loss to explain how an iteration of Trixie obtained Alicornification and was able to leave a Wound That Will Not Heal on her.
Unicorn Interviewer: That's the biggest irony of them all. Those that seek Godhood without knowing what it truly means. Those like Chrysalis...they only see the vague outline, not the complete whole. They see power, and that's it...And Chrysalis is now seeing the price of divinity. Discord is the only God with no compassion for life at all, and even he had an innate capacity for it he buried over the eons...Even the End of All Things includes an End of All Suffering...
Played horrifically straight when it comes to Nightmare Eclipse/Paradox compared to Discord. We see from past loops Discord saw her as a momentary distraction and wasn't that concerned about her in the early loops, only on getting her out of the way so he can continue his games, perhaps even happy to have 'start overs' when he lost. Cut to several hundred million years worth of time loops later, Discord's little more than a tortured Puppet King who considers being killed several billion times by his family as punishment for his crimes relaxing compared to the torture she put him through and is only still evil because she won't let him perform a Heel–Face Turn. Paradox herself? An Omnicidal Maniac who's erased Dark World and everyone in it so many times she can't even remember how it started or the names of any of the 'NPCs' she's Ret Goned. Inuniverse, everyone who knows what she's done justifiably considers her worse than Discord, including Discord himself.
Evil Is Hammy: Judging from the trailer, Discord, Loneliness and the Serial Killer obsessed with dolls are all set to be this in the audio version of "Reharmonized".
Evil Overlord List: Brutally (and hilariously) deconstructed during the Dark World Series, when the Seaponies put on a show about Discord's war with Grogar — Grogar apparently followed the list to the letter, but Discord just took advantage of the new pattern that was created used every rule against him.
Evil Parents Want Good Kids: Surprisingly, Dark World Discord feels this way about his daughter Fluttercruel. Justified, as he himself is no longer evil but forced to remain as such by Eclipse, so he tries to get his daughter away from her destructive impulses.
Evil Versus Evil: Narrowly subverted. Under the stress of Discord's mind games, Luna comes dangerously close to turning back into Nightmare Moon to fight him. She manages to avoid giving in just in the nick of time before she could completely lose herself to the darkness.
At some point in the Dark World timeline, Grogar returned and once more tried to conquer Equestria, leading to a war between him and Epilogue!Discord. Given their respective M.O.s, this also qualifies as an all-evil example of Order Versus Chaos.
Also from the Dark World, the Master vs the Valeyard at some point in the past.
Another Dark World one: Lord Tirek vs Nightmare Eclipse happened in several loops. Apparently it was always a tie, ending with the planet's destruction in the ensuing battle.
Another subversion in Shining Armor 18.1. It turns out Minuette is the Master using a fob watch. The Master tried to convince her to open the watch during Makarov's war so he could defeat Makarov. However, Minuette manages to resist opening the watch.
Queen Cocoon vs Chrysalis in Chrysalis' Origins Episode. While Cocoon did make Chrysalis a slave and was in general a terrible ruler who almost destroyed the changelings by pure incompetence, Chrysalis was still a budding Sociopath with a considerable body count by that point in time. Chrysalis even says she's not opposing Cocoon because Even Evil Has Standards, but because she's disgusted with Cocoon's incompetence.
As shown in flashbacks, Queen Chrysalis vs General-AdmiralMakarov. While Chrysalis puts up a good fight, Makarov ultimately won by simply Rewriting Reality and erased the Changelings from existence until Shining fed him to the Wolf. Also counts as a pure evil version of Cain and Abel, as they're technically brother and sister due to both being made by Pandora.
Discord said that Cloudsdale wouldn't collapse if Rainbow Dash went to rescue it. It didn't, Discord drove them all insane and made Rainbow Dash watch.
Just after having told everyone in Cloudsdale, very loudly, broadcasting a huge picture of Rainbow Dash in the process, that Rainbow Dash was the one who saved Cloudsdale by dooming the rest of Equestria.
Cheerilee tells the foals in her care "the Princess" has ordered them brought to her castle for safety. She never said Celestia or Luna's name and she turns out to be The Dragon for Princess Gaia, possibly of her own free will.
When Applejack looks into the Truth, we see a large number of alternate universes, including the Bad Future presented in epilogue. In a subversion, Applejack is actually heartbroken by the fact the children she had in the "Orangejack" universe won't exist because she didn't take that path. Celestia reassures her that they do exist in that timeline.
In "AJ's Dreams" many other alternate universes are seen (including several ones where other members of the Mane Cast have become Nightmares or are otherwise evil/crazy). At the end of the battle against Nighmare Mirror (herself an alternate version of Applejack), Applejack and Orangejack meet many alternate versions of themselves, including ones that bear different Elements of Harmony (Orangejack herself can bear the Element of Generosity).
Defied for Nightmare Eclipse/Paradox. She discovers after her final defeat that her fusing with every Nightmare Purgatory at birth means that all other Nightmare Eclipses that could/will/did exist share her same fate, meaning there are no alternate timelines where Eclipse wins.
Expy / Generation Xerox: Magica, a brave filly from the Dark World killed during the raid on the ponies practicing magic in Ponyville, bears a number of similarities to Trixie — and her name fits the next-gen naming system.
Face Death with Dignity: Mimic can be seen as doing this. Instead of running and hiding, she sacrifices herself to hold off Discord, knowing she'll die but happy she saved her friends and daughters.
The G2 Mane Cast more or less accept their fate's with dignity in the end, at least the ones who saw it coming. Clover is the only one who refuses to accept she's dead.
Dark World!Pinkie Pie realizes after being purified, her Element of Rage is dying and thus decides to devote what time she has left to protecting her friends and loved ones and helping save the world.
Princess Luna in her second sidestory. Driven by her protectiveness of Pipsqueak, Luna confronts Celestia over what should and should not be "natural," and leads her to accidentally kill Pip. She then raised Pip as undead and tries to murder Celestia, killing several ponies in the attempt. Fortunately, it was All Just a Dream.
Fake-Out Fade-Out: Pinkie manages to do a version of this at the end of Clover's Gaiden chapter by bringing the group back when it looks like the scene was over so she can arrange for Princess Gaia's G3 village to be completed as an amusement park.
Fake-Out Opening: Several chapters begin with a fake title designed to hide the true nature of the chapter from the viewers, the real title only revealed after The Reveal. Normally the fake title and beginning of the chapter hides a rather serious chapter:
Nights Princess Luna is actually "Nights: Luna's Nightmare" and depicts a nightmare Luna has about turning evil again over Pip.
"Happy Cake Adventure" is actually "Generational Transitions Part 1", which shows us an apocalypse.
"Party At Canterlot Caste" is actually "Daybreak", as it depicts the transition between the Darkest Hour and things in the Dark World starting to take a turn for the better.
Some of the upper class Earth Ponies in Ponyville have some degree of racism towards Unicorns and Pegasi, including Diamond Tiara's family.
There's also some degree of racism towards mixed race unicorns among pure blooded ones. Trixie really hates this one and is implied to have been a victim of it. Her dream world has all things promoting this are ordered to be destroyed and she nearly loses it when called a half-dirt unicorn.
Surprise, surprise...there's also racism towards Earth Ponies as well according to Word of God stated here.
It's implied that this is far less rampant than is previously suggested in the story (at least not in the middle- and lower-classes). Trixie exaggerates its prevalence to justify her lying about her true nature.
Changelings have this towards non-Changelings, who they call cattle. Though some Changelings have realized it's horseapples. Ironically, it turns out that Changelings are ponies, making this actual racism instead of speciesism.
Cattle is used by Changelings towards nonchangelings.
Fantasy Counterpart Culture: Many show up in the Shining Armor Arc (fitting as the show proper has alluded to places like Saddle Arabia and so on).
Fantasy Pantheon: The world has a rather sizable Pantheon, which includes Celestia, Luna, and Discord. There were actually 20 Alicorns and 5 Draconequi all of whom are Physical Gods while there are four Elders who are real gods. Alicorns are referred to as Nature's Law and Draconequi Nature's Fury. Due to just how many of the Alicorns there are, only one other than Celestia, Galaxia, gets a main role at any point, but Word of God has given them all names. The others are Abbatissa, Imperatrix, Cadence, Rota Fortuna, Justitia, Venus, Leo Fortis, Turris, Mortis, Pensilis, Currus, Morning Star, Eremo, Puerillis, Princeps, and Judicium. The Draconequi are, other than Discord are Destruction, Strife, Pandemonium, and Anarchy. The Elders are Havoc and Entropy, the parents of the Draconequi, and Fauna Luster and her mate (not named in story), the parents of the Alicorns.
It may be even larger than that, considering the existence of Ponythulhu, Queen Tiamat (the mother Goddess of the dragons), and possibly Father Deer (the alleged god of the Hooviets but it turned out it was just a front for Makarov, the big bad of the Shining Armor arc.). A deer goddess of some sort appears in Bright Eyes' Gaiden story as well, who is later turned out to be Mother Deer from the Shining Armor arc.
We get another group in the form of the Outer concepts, of which Ponythulhu is a part of. As you can probably guess, these are based on the cosmic monsters of Lovecraft's Cthulhu Mythos.
The Federation: As shown in Shining Armor's arc, Equestria's neighbor and ally the United Republics of Colombia (obviously an expy of the United States), which started out as an alliance of many of the griffin clans (though not all of them). Though that said, there's a large population of non-griffins — heck, many of their presidents have been ponies, with at least one zebra and a minotaur holding the office at some point.
Fever Dream Episode: Shining Armor 21 starts as one of these, Shining coming down with a nasty illness... On the day of Chaos as Discord escapes.
Gaia Festival: A n-day(we don't know how many days it lasted) festival dedicated in celebrating the good that came out of Fluttershy's brief reign as Princess Gaia/Nightmare W Hisper. The reason Princess Celestia created the festival was not Fluttershy's dangerous actions just happened to create some good, but because that Fluttershy did not completely lose herself to the darkness, as she did try to do good in creating a better world, with her kind heart willing to sacrifice her own happiness for the sake of everyone else.
Fiery Coverup: In the Shining Armor arc, break-ins at the Embassy and a University in Zebrawa were mainly aimed at destroying something using an advanced and unrecognised incendiary device (Implied to be a type of thermite), and seemingly succeed... but could just as easily have actually stolen the "destroyed" items. Not to mention that four others after whatever was at the university attacked a lab assistant, and then were found dead: the skilled nature of how they were killed revealing a lot more about the skills of the people breaking in than anything else.
Princess Gaia's songbirds are explicitly stated to be a part of her, and she doesn't seem to be all that upset by their loss.
It turns out that the Princess Gaia the Mane Cast were talking with was just an illusion of the real creature that she'd become, Nightmare Whisper.
Havoc did this during the Alicorn/Draconequi War, as His true power made it impossible for the true him to directly take part. Said Avatar went insane and was eaten by Discord.
This is apparently a trait all Gods have, with Luna being particularly adapt at it. Moonlight, the foal form she uses to spend time with Pip, is an Avatar.
Chrysalis is also capable of a form of this (which makes sense, considering she was born from Cadence's discarded Shadow) by infusing one of her minions with her essence, giving them a large power boost and her the ability to control them directly, but them being much weaker than the real thing. She first used this to trick Makarov during their fight.
In a bit of irony when Cadence finally fights her, it turns out to be a case of Chrysalis' variant...then it's revealed Cadence was using an Avatar as well, having been instructed on how to do so by Twilight.
The Final Temptation: An edit to Bright Eyes' Gaiden chapter has Cruel Eyes/D__t's Shadow try to do this with one simple sentence as his last attempt to get her to see things his way. Bright Eyes still turns him down, but admits that it hurt to do so because of how much she wanted it.
Cruel Eyes: But Starlight would be alive again because Patch believed she was still alive.
First-Name Basis: Rarity's full name is Rarity Belle, but she doesn't go by her full name much at all, even professionally.
Dima only refers to General Admiral Makarov by his first name Solomon, stating Makarov is a name given in honor, and Makarov doesn't deserve it.
Fission Mailed: When the sheer despair of Nightmare Whisper threatens to Discord Twilight, the story seems to abruptly end...
A/N: Meh. I think I'll just end the story there, in fact, I think I'll end the entire series right here. Who actually cares about this series anyway? It's all just garbage. Nothing but fan service and rip-offs. And I'm just tired of the whole thing anyway. It's not like anyone would NOTICE if this series suddenly stopped.
Only for Trixie to restart it by using the memory spell to pull Twilight back.
Dark World has a scene were it appears Nightmare Paradox wins, kills the Mane Six, and gets Twilight to replace her. The scene cuts to Pinkie Pie and company still playing the video game version, implying this was either them losing the game. There's also glitches in the scene, such as Fluttercruel being presence when she's dead, meaning it may have simply been a previous timeline.
The Hero: Twilight Sparkle, the leader of the group.
The Lancer: Trixie Midsummer, originally the Sixth Ranger, she upgrades to this by the finale of season seven. She's the second Element of Magic and her hamminess and reliance on guile serve as a foil to Twilight's calmer nature and status as a magical powerhouse.
The Smart Girl: Applejack. After looking into the Well of Truth, she essentially becomes the most voice of reason on the team and the most level-headed.
The Big Girls: Rainbow Dash and Rarity, the two best fighters on the team and the only ones with actual martial arts training.
The Chicks: Pinkie Pie and Fluttershy, the quirkiest, and the gentlest member respectively. They're are also both The Heart of the team.
Fix Fic: Sort of. The fic doesn't change canon events, instead it writes around them, providing background information that explains the events of the canon a bit better using details from the fic's canon. For example, Fluttershy was terrified on Nightmare Night thanks to Fluttercruel joking around with her and Rainbow Dash's behavior in the "Mysterious Mare-Do-Well" was trying to cover up her Heroic B.S.O.D. over how she dealt with Discord's Sadistic Choice. The author typically updates after a new episode has come out to fit it into the fic's canon. Thus far, it's actually a pretty good example of doing thisright.
An in-universe example: Pinkie Pie tries to repair the damage Discord caused to the other ponies (and especially herself) by taking her normal personality and cranking it Up to Eleven, partying continuously without sleep for almost three weeks. During her Battle in the Center of the Mind, Pinkamena helps her realize that she has been essentially flanderizing herself since she got her cutie mark by splitting off those parts of her personality she didn't want to deal with. Upon realizing this and under attack by her own anger, Pinkie performs a Split-Personality Merge and finally frees herself from Discord's influence.
Another in-universe example: in the "AJ's Dream" chapter, Luna explains that ponies turn into Nightmares when they allow one facet of their personality to consume them completely.
Fling A Light Into The Past: During a fan sequel to Epilogue, Twilight Tragedy uses a spell to send her thoughts back in time, warning her past self about Discord's trap and reminding her about the lessons she learned about friendship, thus enabling Twilight Sparkle to overcome her trials and set in motion the events of the main series.
Foil: Ironically, Fluttercruel manages to be her own foil. Epilogue!Fluttercruel is heavily implied to be a monster whose deeds ware so terrible that Twilight Tragedy refuses to tell us them (despite being perfectly willing to describe every other horrific detail about Discord's reign). This only serves to show how much of a jerk present Fluttercruel isn't in compairson to what she could have become.
In Shining Armor 16 Part 2, General-Admiral Makarov forces Shining to what him deliver a No-Holds-Barred Beatdown to the rest of Misfit Actual, including subjecting Thunderchild to Electric Torture and blowing Running Gag's wing off. Worse? It's revealed in the end that he was allowing Cadence to watch the whole timethrough a song bird before shooting it.
Taken Up to Eleven in 17.1 when Makarov forces Shining to watch him start his world war, commit genocide, and try to kill Twilight. This backfires when he pushes Shining too far, however.
This was more or less how it was for Applejack while under Chrysalis' control, as she was completely aware but could do nothing about it.
Foregone Conclusion: The fact that the G3 Universe dies and Celestia/Star Catcher was unable to stop Strife had already been established before "Generational Transitions" started. Doesn't make it any less of a Tear Jerker though.
In "Origins", we already knew Discord becomes Evil Overlord of Equestria, Mimic dies fighting him and busts out his tooth, and Celestia and Luna discover the Elements to defeat him. How it all got to that point, however, is pretty interesting...
The third chapter of Dark World is a flashback to Queen Cadence'sLast Stand against Discord and the corrupted Mane Six. Since it's a) a flashback, and b) the Epilogue timeline, we know that she's going to lose and die. Which she does.
Seeing as Shining Armor's arc is his backstory and explaining where he's been during all the events leading up to present (and he had a very small cameo at the end of Mind Games), we know he's going to survive everything he goes through. It turns out to be subverted, as Shining's Immune to Fate status means he's in the past trying to catch up to the present, meaning it's Shining's present. As a result, Makarov could actually win and Shining's survival isn't assured.
Discussed and subverted in Dark World pertaining to Rancor knowing Twilight in the future (from Twilight's perspective). Both Nightmare Paradox and the Benevolent Interloper state this does not mean Twilight and company are destined to defeat Paradox and Paradox could just as easily give Rancor the ribbon after winning, meaning the future is still in flux.
In the "Black Pearl" chapter, Luna describes how ponies who join the royal guard are gifted with a minute fragment of their commanding princess' essence, undergoing some physical changes as a result. This is exactly what happens to Cheerilee when she becomes Princess Gaia's Knight, and Ditzy Doo is offered the same position a little later.
When Rainbow Dash becomes unable to handle the fact that loyalty toward one thing means betrayal of another, she begins to transform into a Nightmare, but her friends are fortunately able to talk her down and return her to normal. However, when Fluttershy cannot deal with the cruelty inherent in nature, her friends are not there, and she transforms into Nightmare Whisper.
During her transformation, Fluttershy is shown growing blutterfly-like wings. When we first see Princess Gaia, she's described as having feathered wings, forshadowing the Princess Gaia we see isn't the real one.
Princess Gaia: "Oh sweetie my sweet little foal... mommy already feels the price for everyone else's happiness. So don't go worrying your little head over some arbitrary cosmic balance my little foal, let mommy worry about it."
Early in the Final Battle against General-Admiral Makarov's forces, Shining survives a sniper round to the chest thanks to the armor Pandora gave him. Later, Gilda gets shot in the chest by Makarov's Desert Deer Pistols. While it still mortally wounds her, the armor weakens the blow and lets her to hang long enough to destroy the Iron Curtain.
"Different From Everypony Else" has Celestia casually comment that if an Alicorn explode, they'd split into three ponies, each from one of the tribes. At the end of Dark World, Amicitia blows herself up, creating the Interviewers (and Shining Armor).
A subtle one. When Dark World Twilight ascends, she's told certain parts of a mortal are removed and new parts added when they ascend to make them fit for the job. During the Wedding, Chrysalis becomes an Alicorn, and as a result gains a heart.
In "AJ's Dreams" she sees an image of a filly wearing gray and pink armor with Nightmare Diamond's symbol on them. Guess what Alula and Tootsie are wearing for the final fight with them? Though in the vision, it was implied to be Silver Spoon, who isn't present.
Applejack learns what could have happened had she remained in Manehatten: Big Macintosh would have taken up the Element of Honesty and become part of the Mane 6, while Orangejack would have embraced different talents, had a different Cutie Mark, and eventually been Happily Married and started a family.
Luna telling Fluttershy how, if she'd behaved a little differently, her paradise might have been closer to being achieved and she might have even come out OK from it. We even see an Alternate Universe where she took Applejack's suggestion of being honest with her followers, with their support allowing her to conquer the suffering she'd sealed away.
Forgiveness: One of the overarching themes of the Dark World Series.
The Father of All Alicorns also gives this to the truly repentant, even saying the above mentioned Arc Words to Starlight after she states she doesn't deserve forgiveness.
It's stated in the Shining Armor Arc that ponies take forgiveness QUITE seriously, to the point that saying something is unforgivable carries a lot of weight and he only declares Makarov's actions beyond forgiveness after seeing him attempt to slaughter an innocent village and condemn ponies to an And I Must Scream fate as his Co-Dragons.
Forgotten Fallen Friend: Subverted. Character deaths are never just brushed under the rug and typically have long lasting effects on the survivors, on top of being mentioned long afterwards. This even applies to secondary characters. Ranger and Sunset's deaths continue to effect their friends well into the Wedding Arc, with Garnet's fear of her or Gag dying before their wedding day stemming from this trope.
For the Evulz: In one of the Mind Games chapters, Discord sings a Villain Song about why he does what he does. After going through some rather silly reasons, he basically sums it all up with, "Why do I really do it? Because I can."
Chrysalis, being a sadistic sociopath, indulges in this, but is typically far more pragmatic about it than Discord. She gradually does more and more of this as she has a Villainous Breakdown.
For Want of a Nail: Apparently, the nail was Twilight. From what can be gathered, the only thing different between the "Epilogue" timeline and the Reharmonizing timeline is in the Epilogue timeline is that Twilight broke in the maze while she didn't in the real one. One piece ofRecursive Fanfiction explores how this might be possible. Discord was playing a "game" with Celestia that if he broke all the mane cast in one goal, he'd turn Celestia and Luna into gold and silver statues. In Epilogue's timeline, he succeeded, meaning that Celestia and Luna were turned into statues before Luna could send Twilight her letters back so she could save the world.
It's eventually revealed that Shining Armor is the nail because he literally did not exist in Dark World and was inserted into the timeline by Amicitia, Dark World!Twilight's Alicorn self, to create a divergent timeline where Discord was defeated. His existence gave Twilight the emotional support needed to do the above and enable Discord's defeat.
Also, the other nail is Applejack. Due to her insistence in this story that the truth always be faced head on, this changed the plot of "The Last Roundup" DRASTICALLY, so that the reharmonized timeline had to break off from the heart world to become its own universe.
Discord's decision to utterly break Trixie is arguably a third. The aftermath basically derails the episode "Magic Duel" in its entirety.
Rancor's advent in the Dark World was this to the "Groundhog Day" Loop, throwing things so far off Nightmare Eclipse's script that it allows Discord to throw another wrench in the works and force Eclipse to expose herself to the mane six.
After Dark World!Twilight became Princess Amicitia Zorya Spes Equestria, a Physical Goddess and one of the Major Arcana, this is how she gives the Fix Fic treatment to numerous grimdark stories, including Cupcakes, Rainbow Factory, Cheerilee's Garden, and Pages Of Harmony. Or at least the Pony POV Multiverse counterparts. For Cupcakes, she has Gummy be a Spanner in the Works that knocks the stale cupcakes with a parasprite larva in then to the ground, and when Pinkie Pie is tempted to eat them anyway, she gives her a reminder that she was raised better than that (keeping her from ingesting the larva, which would have driven her insane). For Rainbow Factory, she gives Rainbow Dash the courage to report how rainbows are really being made to the authorities. Unfortunately, while Rainbow Dash is hailed a hero in Equestria for doing it, She's seen as Cloudsdale's Biggest Traitor for her actions For Cheerilee's Garden, she has Berry Punch and Ruby pay Cheerilee a visit for some impromptu counseling. And for Pages Of Harmony (possibly, Word OF God is vague which mad scientist Twilight it's supposed to be), she tells Twilight Sparkle that she would lose far more then she would gain by vivisecting her friends, which convinces her to tell Spike to get her some professional psychiatric help.
Dark World!Celestia and Dark World!Luna both had this done to them by Discord, Celestia more than Luna due to Laser-Guided Amnesia.
Four Lines, All Waiting: The fic actually went through this for a couple years: In line 1, we have Shining Armor's backstory (which Alex has stated will eventually get to this series's version of the events of "A Canterlot Wedding"). In line 2, there's the Dark World story trying to give the "Discorded Ponies" series a happy ending. In line 3, we have the side story that tells the tale of the main G2 ponies both when they entered G3 and After the End of G2. In line 4, we have the Reharmonized Series proper, currently on hold with Discord about to be released, while the back and side stories finish up.
As of January 2014, all the different lines apart from the reharmonized series have finished up.
During the battle with Nightmare Whisper, Twilight attempts to use the memory spell to help Fluttershy. This backfires and results in a mental attack so devastating that the author considers giving up writing the story. Thankfully, Trixie breaks both Twilight and the author out of it.
Happens again in "Butterflies" when Fluttercruel knocks out one of the interviewers for getting a little too personal with the questions.
The author likes responding to comments by writing them as if the characters themselves were responding to reader comments and questions. Sometimes entire role-playing sessions arise from this, to the point where some readers will actually ask the author to have the character in question respond to the part of the comment that's directed at them. Conversely, some readers find it really, really creepy, particularly when he does the role-playing as one of the villains (or Chrysalis's brainwashed victims during the Wedding Arc), and will sometimes ask that he NOT respond with a role-play comment.
Fridge Logic: In-Universe, this is Makarov's biggest weakness, as pointing it out gets him furious and weakens his powers.
This is also the weakness of Discord and his cousin's Rewriting Reality spell. The CMC pointing it out can help break victims free.
The characters' motivation for fighting Nightmare Whisper is not necessarily that what she was doing was terrible (as the characters had different opinions on that) but rather to save Fluttershy from herself. This is especially true for Rainbow Dash, Rarity and Fluttercruel, as the former two decide that they must try to kill their dearest friend (as they figure that Fluttershy would rather be dead than see what she has become and that they are good enough friends to do what must be done to help Fluttershy) and Fluttercruel will stop at nothing, sacrificing herself if necessary, to see Fluttershy restored to her former self.
After the battle with Nightmare Whisper, the heroes convince Fluttershy and Pinkie Pie to release pain and suffering back into Equestria so they wouldn't have to see their friends endure the torment any longer. Once again, there is disagreement among the characters whether or not this was the "right" choice, but not a single one of them is sorry that Fluttershy decided to let go (though it is hinted that Pinkie felt that holding on to everything should have been her responsibility, rather than Fluttershy's).
Friendly Neighborhood Vampire: While love vampires instead of blood ones, several Changelings have been shown to take this route after defected from the Hive. This includes Bon Bon's 'sister' Moth and a trio of Equestrian Guards named Weaver, Diver, and Bombardier (who invoked this trope to try and prove Changelings didn't need to be monsters). Instead of stealing love, they choose to pacifically feed off the freely given love of their genuine loved ones, who are unaware of their status until the Wedding Arc. After Cadence overthrows Chrysalis and becomes Changeling Queen, the entire changeling tribe becomes this trope.
It's also heavily implied one of Scootaloo's parents was one of these Changelings.
Friendly Sniper: Private (and later Lance-Corporal) Captive Audience from the Shining Armor Arc. Despite being a skilled sniper, he's also a nice guy who Shining would have no problem if he wanted to as Twilight out.
Natasha, a Deer Sniper, is another example. She's generally polite and easygoing, but is probably a more serious sniper than Audience is.
From a Certain Point of View: During Onyx Tiara's discording, already surrounded by lookalikes of Golden Tiara, he rejects : Screwball/The real Golden Tiara with the words: "Begone, parody!", which is correct, if one were to interpret the 'thing' as acting completely different from lookalikes posing as his wife.
The Pegasus Despot from Patch's entry in 7 Dreams/Nightmares — before the collapse of G2 society, just some fat nerd. Afterwards, the Evil Overlord of a city, ruled by the brainwashing power of a fragment of the Rainbow of Light.
Invoking a heroic version of this seems to be the Pantheon's entire plan to counter Discord's endgame, choosing 'nobodies' Discord and company overlooked to give the means to fight back knowing Discord wouldn't see it coming. The best one could be AK Yearling being given the opportunity to become a real life Daring Do, since as far as Discord is concerned, she was just some random bookworm he 'played' with once.
We see some of one of Twilight's possible future selves when Applejack looks into the Truth and she most certainly qualifies. Especially when Applejack hints, while talking to Nightmare Whisper, that Twilight is possibly the pony destined to defeat death.
According to some documents and ID cards from the human world recovered by Misfit Actual and The Doctor, Megan Williams' sweet little sister Molly (or perhaps an alternate version of her), grows up to be a Special Forces agent.
The Nameless Passenger turns out to be Dark World!Twilight's potential future self and Superpowered Evil Side Nightmare Eclipse/Paradox. She's so consumed by her desire for revenge, she's turned Dark World into a "Groundhog Day" Loop to torture Discord for eternity, not caring how many ponies pay the price in the process. She even refers to Twilight as 'myself' or 'me' and desires to force her to become her to continue the cycle. To say Twilight isn't happy with this potential future is an understatement.
Dark World!Rainbow Dash has this reaction to encountering her own Nightmare, Nightmare Manacle, among Paradox's Psycho Rangers.
Gate of Truth: Well...the Truth. However, it seems there's little to no way to actually control what knowledge you get, and staring into it for too long can have nasty side effects. Applejack's staring into it ended up turning her into a Living Lie Detector.
Gem Heart: The Dark World!Mane Six have the Elements of Chaos replacing their hearts.
Tom, being a stone statue given life, has one as well.
Genius Bruiser: Dark World!Spike, while now a fully grown and super strong dragon, has also had a thousand years to read up on multiple subjects, including fighting styles and tactics. This especially shows up in his fights with Tom and Rancor.
Professor Kabuto is this. Not only is he one of only three characters smart enough to complete Chrysalis' rune, his alterations to himself make him so powerful Chrysalis' trap for the Mane Six going after him was him.
Genius Loci: Discord's palace in Dark World. Earlier it was implied to have some degree of awareness in how it rearranges itself, then it was confirmed later it's fully sentient with desires of its own and even capable of being reasoned with. Applejack manages to reason with it so it will remain a neutral party in the upcoming showdown with Discord, in order to prevent another hedgemaze situation. It even does a Pinkie Promise.
The realms of the Four Elders are all extensions of themselves as well. According to Word of God, anyone you encounter in Pony Hell may either be another doomed soul, or Havoc just playing around.
Genre-Busting: This is a Fantasy/Action/Psychological Drama/Meta-world Building/Philosophical/Coming of Age fanfiction
Glamour Failure: Princess Gaia's illusion is nearly perfect, convincing all of her friends of who she is. Even the Element of Honesty cannot find any lies when looking into her eyes. That is, until Applejack realizes that she doesn't see any truth in Gaia's eyes, either.
Twilight Sparkle manages to break free of Loneliness' illusion by realizing the "doctor" talking to her mentioned three friends, not five, and didn't realize Twilight was Princess Celestia's apprentice, something any true doctor taking care of an insane pony would know.
Twilight had recent experience with actual insane asylums while helping mental/psychological casualties of the Day of Discord. And soon recognizes this "asylum" and "doctor" as being Theatrical versions; the sort of things a showpony with no actual experience would portray.
In Luna's second sidestory, some things are intentionally off in her nightmare or don't make sense as a version of this for the reader, foreshadowing the reveal that it's All Just a Dream.
God Is Flawed: Celestia and Luna are both flawed beings who have made their fair share of mistakes. Luna, however, tends to need to be pushed a lot harder to actually admit to hers, another of her flaws. Subverted, at least by Celestia and Luna's word, with their Parents.
God Is Good: Evil deities are an exception, not the rule, in this universe, and even then the Outer Concepts are the only ones malevolent by nature (and most of them are just meant to be scary to prevent people from going too far in the name of progress rather than being genuinely evil). The deities even call those of them that Fall Devils and Demons specifically because they threw away the thing that made them deities in the first place. All in all, the deities genuinely desire to help life grow and succeed, even if in some cases they're harsh. The writer has repeatedly said he hates the 'Gods are always bad and need destroyed' treatment by many works of fiction and actively tries to avoid it being the case in his universe.
The sidestory depicting Pinkie Pie's backstory and how she knows of the G3 timeline has Anarchy, Discord's brother, and an alicorn rewriting the G3.5 universe into the G4 universe, erasing several ponies from existence in the process and warping others into new versions of themselves. This is a last resort to stop the universe from ending all together and the alicorn explains to Pinkie Pie this was the last resort option.
On top of that, Destruction's subsequent triggering of a Class 2 Apocalypse of the G2 world to prevent the Class X-4 Apocalypse that happened in the G3.5 universe from ever happening.
During the battle with Nightmare Whisper when she and Rainbow Dash are essentially the only two heroes still standing, Twilight Sparkle, at a complete loss as to what she can do, begins reciting the lessons about friendship that Fluttershy has learned with no expectation that anything could come of it. Fortunately, Fluttercruel hears Twilight and realizes that Fluttershy needs help.
Celestia during Luna's nightmare, when Luna turns evil again and tries to kill her. After nearly being killed herself, begging her sister to stop, Celestia is left with no choice but to fight back and try to kill her rather than let Equestria be ruled by a tyrant.
The existence of the SAS (Equestrian Black Ops, essentially) is built on this — due to the ponies' natural dislike of violence, the SAS' stance of "shoot first, ask questions later" is an absolute last resort.
Celestia states that a situation being dire enough for the Elders to interfere directly in the mortal plain would be such a case due to such a disaster needing to outweigh the amount of collateral damage one of them would bring with them by doing so. To put this in perspective, the Windigos and Discord wasn't nearly close to that threshold. Not even Nightmare Paradox qualifies, and Fauna Luster states that only a threat to every timeline and universe would be enough to outweigh the collateral damage of an Elder's direct intervention.
Sensing Nightmare Eclipse/Paradox causes Dark World!Luna to ask Rainbow Dash to fly her and Celestia up into space so they can recharge directly from the sun and moon (having been completely drained during their imprisonment), something that's extremely dangerous, even for an infinitely regenerating immortal like her (hence why she hadn't even considered doing this before then).
It turns out that Equestria actually has a specific protocol for when this has been crossed and the Princesses' direct intervention is to be called for, including Kaiju attacks. Fittingly, it's called Article 1954.
During the Wedding Arc, things get so desperate that Twilight and Cadence seriously consider the possibility of releasing Discord to fight Chrysalis, but only as an absolute last resort.
Golden Age: The civilization presented in G2 is treated as this for Ponykind before it unfortunately ended due to Destruction having to nuke the world to advert a worse apocalypse from happening. As pointed out, the G4 civilization is just now starting to recover some of the capabilities they had, while others are still far off.
Turns out this happened on both sides during the Final Battle of the Age of Myths (G1). Hydia called in her entire family while the Paradise Ponies called in every single ally they'd made during the course of G1 in response from Katrina onward.
Good All Along: Well, more like Chaotic Neutral all along but still. Discord's brother Anarchy seems to be an antagonist throughout a Loose Canon Side Story... Then it's revealed he's only doing it because he has no choice and the universe is on the verge of entropy if he doesn't. Subverted with Discord, who is revealed to be a Jerkass even by Draconequi standards and is busy turning Flutterponies into parasprites For the Evulz at the time.
It turns out the apparent Hooviets that had been following Shining around in scenes were actually Anti-Hooviet Rebels trying to get ahold of him. They were simply using Psychic Static that made them appear to be Hooviets due to Makarov's powers.
Good Feels Good: Trixie quickly discovers at the party Pinkie Pie throws for her that she actually likes having the mane cast as her friends who honestly like spending time with her for who she is (except Rainbow Dash at first, but even she warms up to Trixie). There's good reason she sings the My Little Pony: Friendship Is Magic theme with the mane cast.
Good Thing You Can Heal: The Dark World!Mane Six are immortal, having a very effective Healing Factor (destroying or removing their Element of Chaos is the only thing that can kill them). As such, when three of them are redeemed, they have no problem using themselves as shields for their non immortal teammates or making use of their immortality in other ways. This comes in handy since Rarity and Applejack's abilities both require taking someone else's injuries onto themselves, which are promptly healed by their regeneration.
Grand Finale: The in-progress Season 8 and its Final Battle against Discord and Nightmare Diamond are this for the series, which is itself Alex Warlorn's swan song as a fanfic writer, at least for MLP if not fanfic in general, as Alex is in his thirties and doesn't want to be remembered for just this.
The first (chronologically speaking) is the tale of how Patch managed to find the 7 shards of the Rainbow of Light After the End. Without her help, Discord's reign would have been much longer and more difficult to defeat, but due to the Windigos, any knowledge or memory of her sacrifices was lost to history and the alicorns.
The second is when Shining Armor saved history from a shadow of existence which was going to turn the world into his own playground. He managed to Ret Gone it and all its impacts on history, but only the gods and the Time Lords will remember the hardships he had to go through to create a better world order.
Finally there's the fact that in Discord's second coming, it was Luna and not Celestia who sent Twilight the friendship letters that saved the world. The two sisters know the truth, and for once, Luna doesn't feel it that important to share the truth with the public.
Groin Attack: Diamond Tiara ended up giving one to Pocket Watch while escaping him in Canterlot.
General Admiral Makarov gave Shining a pretty brutal one during their first fight. Even though Shining was wearing armor, he still got bruising from it. While Played for Drama at the time, it later gets Played for Laughs when Minuette is examining him.
Later, we find out that while he was on a date with one of his ex-girlfriends, he fell asleep in the middle of her boring story, resulting in her giving him one of these. He's grateful she wasn't an Earth Pony.
Fluttercruel takes a Changeling out with one during a fight in the Wedding Arc. She considers the fact Changelings are vulnerable to these important information.
Applebloom does this to a Changeling during the Crusaders' rescue of Spike. Justified because, as Silver Spoon points out, they're fillies and thus kicking somepony 'in the apples' is one of the only ways they can hurt an adult.
"Groundhog Day" Loop: In "New Game Plus", Pinkie references this by saying she only has one chance to get things right with the events of "Mmmystery On the Friendship Express" and can't count on one of these happening.
The final confrontation with Dark World!Discord implies that he's been stuck in one for quite some time.
It's eventually revealed that Nightmare Eclipse is behind it, trapping Discord in the loop as an Ironic Hell. Word of God considers this an Unbuilt Trope of The Infinite Loops (which Eclipse's existence predated), as it shows what happens when a villain is the Looper rather than a hero.
Groundhog Peggy Sue: Nightmare Eclipse is a heavy deconstruction of this trope. She uses the knowledge from the previous loops to sadistically torment Discord over and over again, every loop ending with Twilight becoming a Nightmare, merging with her, and continuing the cycle again. The deconstruction is from the part she's insane and knowingly and willing condemning the world to another thousand years of suffering and giving each loop a Downer Ending.
The Guards Must Be Crazy: The guards watching Discord in the Canterlot Gardens Maze have surprisingly little discipline.
Trixie, being a showpony, is more than willing to resort to underhanded tricks to get the better of the group's enemies. A good example is "playing the villain" to distract Cheerliee by holding a filly hostage to give the others an opening. Naturally she had no intention of going through with it, but Cheerilee didn't know that.
Orangejack: You and big brother dearest are Elements Of Honesty, I'm still a liar.
Guilt-Free Extermination War: Defied during the Wedding. Not only do the Mane Cast and Misfit treat the possibility of killing Changelings as a last resort, Misfit outright tells Digger Wasp ponies don't believe in genocide. In the end, the war is ended peacefully.
Lone Ranger tried to invoke this with his plan to destroy the Changelings and 'wake up' Equestria. Thunderchild has none of it, outright telling him he's insane.
Gunship Rescue: Just when it looks like Makarov's forces are going to kill Shining's squad in Liberty City, Master Chief Spartan shows up with reinforcements and shuttles to successfully fight them off.
Half Pony Hybrid: Fluttercruel is implied to be, spiritually, a Pegasus/Draconequus hybrid, due to being Discord's daughter by Fluttershy. Though since she's Sharing a Body with Fluttershy, her body is completely pony.
Virgacorns (Unicorn/Zebra hybrids) and Hippogriffs (Pegasus/Griffon hybrids) play a big part in Dark World, due to Discord's actions resulting in Zebras and Unicorns gradually becoming one species, Pegasi and Griffons doing the same. Donkeys and Earth Ponies did the same, but it's far less noticeable.
Kweupe, the guide for Shining Armor's stay in Zebrawa, is a Virgasus (a Pegasus/Zebra hybrid). As Shining points out, this is probably part of the reason she has a job as a guide for non-locals.
Ham-to-Ham Combat: Between Traitor Dash and Twilight during the Duel of Tears, after the latter changes into her pegasus form, Half-Light Noon.
Happens again later when Dark World!Rainbow Dash comes face to face with Nightmare Manacle.
Heart Drive: The Dark World Mane Six have had their hearts replaced by the Elements of Chaos. So long as their Element of Chaos isn't destroyed, they have Complete Immortality and can regenerate from nearly anything. Their personality and memories are also stored in the Elements, as beheading only temporarily disables them while they regenerate a new head and their memories and personality are downloaded into their new brain.
Heel–Race Turn: The Changelings (minus Chrysalis) in the Dark World, thanks to Cadence. They're no longer parasites but symbiotic lifeforms who live in peace with ponies and protect them from Discord.
Also happens in the main timeline due to Cadence challenging and defeating her Evil Twin sister Chrysalis/Cadenza to become the new Changeling Queen. Though half of the Changelings actually pulled one of these before she won, as Changeling law specifically states half the swarm needs to agree for it to stick.
Hellish Copter: Most non-Hooviets think helicopters, the favoured Hooviet counterpart to light airships, are dangerous to the crew as well. Sure enough, a fair few examples crash, are shot down, or filled with cheese instead of Petril. Er, Petrol. However, given they're still heavily armed and/or possibly full of armed deer, they're still not taken lightly.
Anarchy, Discord's brother, is actually trying to save the universe along with his kind and the Alicorns and is just doing what absolutely has to be done to stop entropy from happening. In fact, he actually kind of liked how the G3 universe was before things started going dying. It's only because we're seeing him from Pinkie Pie's perspective that he seems to be a villain like his brother.
Princess Celestia in Luna's second sidestory, after Luna turns evil again. Since we're seeing it from Luna's POV, Celestia is portrayed as the enemy, despite the fact she's trying to protect Equestria from the now evil Luna's tyranny. Of course, it turned out to be All Just a Dream.
Seemingly Invoked by Strife, though she and the other Draconequi and Alicorns all count. Her final words to Celestia imply the reason she played the role of the bad guy for the survivors of the G3 world is to give them the chance to fight for their survival because she believes the right to fight for your survival is something no one should have taken from them, even if they couldn't win.
Cadence in the Epilogue timeline, who's become Queen of the changelings and is leading them in a resistance against Discord — since we see things from the POV of the discorded Mane Six, she's seen as the bad guy.
Rainbow Dash practically spends the entire fic up until her True Healing chapter in one of these over how she handled Discord's Sadistic Choice.
Twilight spends half the fight with Nightmare Whisper in one, unable to come up with any plan because they're fighting an already suffering Fluttershy, causing her to freeze up. It takes her inability to act causing Rarity to be seriously hurt to make her break out of it somewhat. It isn't until Fluttercruel's words make her realize the Fluttershy's true motivations that she breaks out of it completely.
Spitfire is in one after both Discord's breaking of the Wonderbolts, including her, and the Wonderbolts' inability to actually do anything heroic when they try to. Rainbow snaps her out of it by reminding her she and the other bolts are heroes in a different way.
Heroic Sacrifice: StarSong sacrificed herself by forcing Anarchy to erase her instead of Pinkie Pie.
Fluttershy is willing to bear all the pain and suffering in Equestria so other ponies do not have to feel it (and also because she accepts it as punishment for her actions). This will probably destroy her, as she acknowledged (when she was Nightmare Whisper) that the pain had killed her twice already. Pinkie later joins Fluttershy in this, both to help Fluttershy bear the burden and because she feels it would be a crime against the Element of Laughter to allow suffering back into the world. Ultimately subverted, as the others are able to convince Fluttershy and Pinkie to let go.
Subverted with Fluttercruel. While it seems like she's going to die after firing the Elements of Harmony at Nightmare Whisper, but Fluttershy saves her.
G3 Thistle Whistle rammed Strife full speed, killing herself but saving Sky Wishes' life in the process. Strife even shows her respect for the act, calling her the "bravest pegasus to ever live" and promising to have Pandemonium compose a sonnet in her honor.
Epilogue!Cadence taking on Discord and all of the corrupted Mane Six in order to give her changeling subjects a chance to escape, and ultimately being killed.
G2 Bon Bon's sister Misty sacrificed herself to save her daughter from the explosion resulting from Destruction sabotaging the world reformatting spell by shielding her with her own body.
Dima does this by Taking the Bullet for Gilda and being mortally wounded in the process. He then proceeds to refuse medical attention to permanently derail Makarov's script by robbing the psycho of the chance to kill him himself, enraging and weakening Makarov to the point Makarov suffers a momentary Glamour Failure.
Minuette attempts this while pulling a combination of You Shall Not Pass and Taking You with Me by feeding the Master to the Blank Wolf to buy Shining time to reach Cadence and save himself and stop the Master from ever hurting anyone again, fully aware that she might be erased along with the Master (since they're kinda the same pony). Subverted in that while she succeeds in buying Shining time and destroying the Master, she survives and gets a life of her own out of it.
Weaver attempts one, injecting herself with Kabuto's One-Winged Angel potion to match him and let Misfit defeat him, being fully aware that without his modifications it'd most likely be fatal. Thankfully, Garnet saves her.
This trope is why Trixie exists. During the Cosmic Retcon of G3, Destruction's pint up urge for destruction gets the better of him when Shadows of Existence try to consume Abra-ca-dabra, resulting in him getting in a massive fight with Magic Star's Shadow of Existence (using the Alicorn Amulet's Shadow of Existence, due to it having become sapient). This battle threatens to kill one of the unborn ponies waiting for the present to catch up with it. To protect her friends from the now out of control deity, she fuses with Magic Star and the Amulet to stop them, knowing that should she be incompatible, a Fate Worse Than Death will result. Thankfully, performing one of these gives her enough individuality to make the fusion work, creating Trixie.
Hero of Another Story: Pretty much every alternate reality mane cast seen in the truth. Laughter!Applejack seems to fit the most, as her adventure was completely different than the mane cast's. Liarjack also qualifies, because we only saw a tiny piece of her part of the Vision Quest, we see the rest later.
Minty Pie becomes this in the latter part of Dark World, undergoing her own serious of adventures in the caverns under Ponyville while trying to reach Discord's castle. We see bits and pieces, but not nearly enough to fully understand what's going on.
Commander Bond from the Shining Armor Arc, who's often conducting his own important work offscreen.
Dima and the rest of the Rebels also count. While Shining was having his own adventure, they've been undermining and fighting against Makarov and the Hooviets offscreen for a while before they finally team up with the main group.
Shining Armor himself qualifies in comparison to the Mane Cast. His story also includes trying to save the world from a reality bendingEquinoid Abomination trying to take over creation.
Luna states at the end of Clover's Gaiden Story that she and Celestia took care of one of the Eldritch Abominationssealed in Tartarus when it escaped, something Twilight was unaware of. We see this in a Loose Canon side story, where it's revealed the Guard was also involved and took down the cult that summoned it. It's also stated either the Guard, the Princesses, or both deal with most of Equestria's problems and the mane six are only called in if the threat requires the Elements of Harmony to defeat.
During the Wedding there are three groups working concurrently against Chrysalis (the Mane Cast, Fancypants' rebellion, and Misfit Actual), but not interacting with one another. As a result, in each of their storylines, the others are this, being mentioned or their actions having an effect, but not actually interacting.
Also from the Wedding Captive Audience and the Doctor's group are apparently on an off-screen adventure in Neighpon dealing with Daleks and Dracozilla. We only get details, but apparently the Daleks were erased from existence (again) and they had to calm down Dracozilla. Also Audience apparently had to save a village from some lizard creature to get his engagement ring for Minuette.
Apparently, according to Dinky the Doctor and her family are helping ponies during Discord's endgame in the Finale Arc. We see this later where the Doctor cures Lickety Split of being a werewolf. Button Lampshades this trope.
He's Dead, Jim: After Minuette destroys the Master, the scene cuts to the Doctor who senses that the Master has been erased from existence and is unable to say his name. He concludes that this time, the Master really isDeader Than Dead.
Hidden Depths: The Shining Armor Arc reveals that Iron Will used to be in the Guard before becoming a motivational speaker.
Applejack's Healing chapter, Discord's love of restoring Twilight's memories to let her suffer before reverting her to her brainwashed state allowed her to write down and hide something during one of these moments. We don't see what this is, but the next scene Applejack sees has Twilight Tragedy talking to Applebloom and Octavia's descendants, now remembering her old self despite still being Discorded. This implies that, even in the universe where he won, Discord may ultimately lay the foundations of his own downfall.
Discord's love of chaos makes him overlook Princess Luna sending Twilight her letters back when she says it's to "give a dragon indigestion", thinking it makes no sense and is therefore perfectly alright for her to do... BIG mistake.
What's better? He was the one that told her she had enough magic left to send a letter in the first place!
Twilight nearly has this happen to her when she tried to use the Memory Spell on Nightmare Whisper. The feedback from all the sorrow Whisper had absorbed nearly drives Twilight over the Despair Event Horizon.
Queen Chrysalis fired the Hoofmaidens and Lyra instead of brainwashed them. While it gets them out of her way, it also allows them to end up freeing Moon Dancer from her mind control without her knowledge.
Professor Kabuto is ultimately beaten when Weaver injects herself with his One-Winged Angel potion and holds him off, then restrains him so Misfit can inject him with a counteragent. This causes him to have a Superpower Meltdown that transforms him into an Earth Pony, which wouldn't have happened if he hadn't had so many experiments done on himself. Justified, as he had no idea Weaver was a Changeling and thus COULD have done that.
Homage: Several to Puella Magi Madoka Magica (of which Alex is a fan), most notably the Nightmares as a whole resembling the Witches in how they're created, with Fluttershy's transformation into Nightmare Whisper mimicking Sayaka's transformation into a Witch and an alternate Rarity having a freak out matching up to Mami's. Nightmare Paradox also has elements of Kriemhild Gretchen. Word of God has admitted the "Groundhog Day" Loop was inspired by Homura's in the series as well.
According to Word of God is that Queen Libra, Rarity's Alicorn self, is inspired off Homura's potential Witch, who was classified as the Witch of the Mortal World...except, you know, she's not evil.
Hooviet Superscience: The Hooviet Empire has quite a few advanced technologies, even by a real world comparison, including tripods and cyborgs. Justified by the fact their leader is a reality bending Imagination Demon.
Star Catcher manages to summon the Rainbow Of Light to use against Strife and Pinkie manages to save Minty from Luna...Then Minty dies and Strife reveals her true strength.
The Dark World!Mane Six are Storming the Castle. They've beaten and redeemed Traitor Dash, killed the Valeyard (causing him to regenerate back into the Doctor), torn apart Discord's defensive line, and manage to convince the Castle to remain neutral in the coming conflict. Just when it seems everything is going their way and it looks like they'll save everyone, it's revealed Fluttershy's essentially dead (though in Pony Heaven) and Fluttercruel is merely using her body. Then during the showdown with Discord's remaining minions, it looks like the heroes have the upperhand, Rarity killing Fluttercruel and Spike gaining the upperhand on Rancor...then Angry Pie rips Twilight's Element out and leaves her to die of Rapid Aging.
In Shining Armor chapter 15, Not The Fall That Kills You, after meeting up with Mother Deer and La Résistance that she was leading against the Hooviets, they had to protect a village from the Hooviets. Shining Armor had just barely managed to protect the village from three volleys fired by all eight guns, then, via a radio they heard Baikal, from the Hooviet army, say that they were starting to run low on ammo...then he said that by run low, they only had enough for two hundred rounds.
Subverted in Part 10 of the Wedding. While Chrysalis does regain control (after getting injured by Celestia and expending a lot of power to repel Luna), the episode ends with Twinkle Shine and company pulling a Big Damn Heroes moment.
Hope Springs Eternal: A major theme in the Dark World Arc, with it being said that as long as there's still hope, there's still a chance to save the world and the only one that can truly destroy someone's hope is themselves.
At the end of the Dream part of Bright Eye's Gaiden story, Zipzee's absolute refusal to give up hope in the face of despair ultimately triggers what Abbatissa, the Alicorn of Prayer, calls the G3 World's last miracle; breaking Discord's spell on the Breezies Discord turned into Parasprites.
Hostile Show Takeover: After Shining was captured in 16, the next chapter has Makarov take over renaming it the 'Cervicorn POV Series Makarov Arc.
How Much Did You Hear?: Twilight asks this of Zecora after it's discovered she was listening to Twilight, Pinkie, and Luna read Bonbon's journal and thus about the G2 and G3 Apocalypses. The answer? All of it. Though it turns out Zecora isn't as freaked out as they expected; she already believed in Reincarnation so now she just knows who she was reincarnated from (Ms. Hackney and Kimono).
Humans Are Cthulhu: The G2 era ponies saw humans as almost divine entities, especially Megan, and are shocked to find there could be evil ones. The Shadows Who Make, Watch, and Rule are said to be the authors, audience, and Hasbro respectfully.
Hypocrite: Rainbow Dash freely acknowledges the irony in how she ignores the good advice she keeps giving Scootaloo about dealing with her perceived betrayal of her friends.
Hypocritical Heartwarming: When Luna brings up Fluttershy's outburst at the Gala, Fluttercruel responds by saying "Hey! I'm the only one who gets to stab Shy' where it hurts!"