Obviously if you've watched the show or read the comics for any amount of time you know that ponies are not without their flaws. They have been known to lie, cheat, and steal, but more often than not there is some mitigating circumstance or reason where (at least in their eyes) there are good reasons for their actions.
That's why for the purposes of this topic we're going to take a look at ponies who have been considered evil. On that note, for brevities sake, we won't be discussing ponies who are simply mean, careless, or con-artists. Only acts of true villainy will be considered 'evil' for the time being (though feel free to bring up characters like Diamond Tiara, Lightning Dust, Suri Polomare, Spoiled Rich, or the Flim Flam Brothers in the comments below).
So let's start with the most recent example of an evil pony: Tempest Shadow.
Evil Actions: Leads the army of an enemy nation to invade Equestria, captures three Princesses by freezing them in stone, and hunts down and captures Twilight Sparkle all in the name of delivering their power to the tyrant Storm King in exchange for her broken horn being repaired.
Treachery is widely considered one of the most evil actions an individual can undertake. It still carries the death penalty in many countries, and even where it doesn't one can expect to spend the rest of their natural lives in military prison. While Tempest was never a soldier of any kind in Equestria, it's clear she bartered secrets about the Princesses for a place in command of the Storm Kings Army. She lead the attack on her homeland without a shred of remorse, only truly coming to regret her actions after the Storm King breaks their deal and reveals he never intended to heal her. It's obvious from this exchange, and the flashback we get to Berrytwist's early life that she herself felt betrayed, abandoned, and ostracized by Equestria when her horn was broken. It's also clear that the Storm King manipulated her with pretty promises in exchange for her turning her back on Equestria. As such, by the end of the movie Tempest sides with the Mane 6 and helps save Twilight and defeat the Storm King. At the end of the movie it's reveal Tempest is kind and caring, who is remorseful for her actions, and she is forgiven. 'Berrytwist' was a good pony who had been manipulated by evil.
Our next example had no dark master that manipulated them to evil deeds, however: Starlight Glimmer.
Evil Actions: Created a brainwashed cult in pursuit of equality and 'true' friendships, stole the cutie marks from the unwilling Mane 6, plotted revenge on Twilight and her friends, and nearly destroyed the present by tampering with the past creating several dark timelines in the process.
As mentioned, Starlight has proven herself a master manipulator and a fearsome abuser of her magical talent. Her original motivation seems to be to create a world where ponies won't be ostracized or looked down on for their differences, but ultimately this is born of her own childhood abandonment issues. When her initial plans are foiled by the Mane 6, she obsessed over their cutie Mark connection and sets out to not just destroy them, but to destroy the friendships that make them special in an act of pure revenge. Though an Alicorn Princess, Twilight finds herself repeatedly out manuevered by the wily unicorn. However, Twilight is eventually able to convince Starlight that her philosophy and actions are wrong, that they are causing far more damage than she realizes, and convinced her to stop seeking revenge and instead seek what she was afraid to pursue again the entire time: A friend. Much like Berrytwist, Starlight is shown to be a damaged pony, though with psychological rather than physical wounds. She takes responsibility for her past actions and apologizes, but she still slips up from time to time and does bad things for good reasons. Ultimately Starlight is a good, but deeply flawed pony who still struggles with fitting into normal pony society. Our next example of an evil pony, however, does try to help her with that: Trixie Lulamoon.
Evil Actions: Insults an entire town for her own aggrandizement, returns to take revenge on them and punish them for driving her out, specifically tortures and enslaved the ponies of Ponyville, and actively attempts to rule them against their will.
Trixie didn't start out as an evil pony, just a subpar magician with a bad attitude. However, when it is discovered that she lies about how great and powerful she is, instead of apologizing for her actions she vows revenge and seeks out the Alicorn Amulet to accomplish this. While it's true many of her most heinous acts are perpetrated under the influence of the artifact that is known to corrupt ponies, it was her will to buy it for the purpose of using it against Twilight and her friends. In the end she is tricked into relinquishing the Amulet, and her first act free of the cursed charm is to attempt to cast a spell that would make Rainbow Dash writhe in agony, which instead only tickles her. Trixie is a jealous and envious pony. Even after she apologizes for going too far with the Alicorn Amulet, she tries to one up Twilight Sparkle by stealing away her student Starlight Glimmer. When this is revealed and Starlight takes offense, Trixie becomes deeply depressed at having potentially lost her only friend. Like Starlight, Trixie is a flawed but not necissarily inherently evil pony. She can be mean, petty, conniving, and cowardly, but she usually will do the right thing if properly motivated. It's hard to say she's necissarily a good pony, but she's hardly evil, unlike our next example: Nightmare Moon.
Evil Actions - Attempted to destroy her sister, destroyed their castle, tried to bring about everlasting night, tried to take over all of Equestria, tormented and attacked the Mane 6 using her dark powers.
Nightmare Moon is often regarded as a separate entity from Luna, the comics even going so far as to imply the existence of a corruptive nightmare force that possesses her in this form. Make no mistake, however, Nightmare Moon is Princess Luna, though a Luna fueled by envy, hatred, and dark magic. It's important to remember that before she became Nightmare Moon Luna stood side by side with Celestia and defeated the likes of Discord and King Sombra. She was a force for justice, who only fell to darkness and acts of evil when she came to feel she was unappreciated and unloved by the subjects she put her life on the line to protect. The focus of her ire fell on her sister, whom she blamed for her situation, and in time she plotted her downfall so that she could reign over a kingdom engulfed in eternal night, dedicated to her as sole monarch. Even after her defeat and banishment she did not back down from this cause, spiriting away Celestia and stopping her from raising the sun. It was only when the Elements of Harmony were used to strip away her dark power that she admitted how much she had missed her sister and how sorry she was that she could begin the long road to atonement and self-forgiveness. Luna is a pony who is a kind and just hero, wise and willing to share her wisdom with the ponies whose dreams she protects. To say she is flawed, however, is a massive understatement, and she faces the long dark night and the nightmares they bring every single day of her life. Luna is a good pony, but her persona as Nightmare Moon is cruel, sadistic, and uncaring. Even so, we see in an alternate timeline made by Starlight that she does not destroy Equestria when she deposed her sister, but instead rules with an iron hoof. Even as an evil tyrant, she protects her subjects from the creatures of the night such as timberwolves. I think this shows that even at her most evil, Luna is fundamentally good... but even the best pony can be warped beyond recognition by their hatred, jealousy, and fear
This brings us to our last's and perhaps strongest example of an evil pony (although he may not be a pony at all): King Sombra.
Evil Actions: Murder of the rightful ruler of the Crystal Empire, Enslaver of the Empire, was fine with ruling through fear and intimidation, spread dark magic throughout Equestria, caused the Empire to vanish on his defeat and tried to resume rule on its return.
King Sombra is an entity of pure evil in the show, who crushes all hope of his stolen subjects, sealing away their memories of how to defeat him, and setting various traps and pitfalls for the unwary who would seek the Crystal Heart. His signature spell seems to be one that forces its victim to live their worst fear as if it were reality, and aside from that the mere mention of his name is enough to send his former slaves cowering. In the comics, however, Sombra is not born a pony but an unbrum, a shadow pony. Despite this he spends his childhood as a unicorn in the Crystal Empire, being raised alongside his friend Radiant Hope, the only clue to his dark heritage being the sickness and suffering that overtakes his body every year when the Crystal Festival is held. When his true origins are at last revealed, and the fact that Princess Amora knew of his true identity while he did not, Sombra lashes out with the dark magic that is his birthright... Killing her for allowing him to suffer and imprisoning his kin. He sets out to free his people, enslaving the citizens of the Crystal Empire to that purpose, and after he returns in the comics this is exactly what he does. In the end Sombra learns that he was manipulated by his mother and he eventually turns on his own kind and seeks to atone for his past actions by finding the fragments of the murdered Amora and bribing her back to life. In the show these events are never referenced, however, and in the alternate timeline where King Sombra is not stopped he enslaved the citizens of the Crystal Empire as soldiers in a war against all of Equestria... his only goal being apparently the domination of ponykind. King Sombra presents a unique dilemma... his comic version is relatable and sympathetic, though he commits truly evil acts, and he ultimately tries to atone for them. However, in the comics he's not really a pony, just an Umbrum in pony form up until the end of his story. In the show King Sombra is definitely a unicorn, and he shows no signs of any inherent goodness or even goodwill. If there is one pony that could prove that ponies as a whole are not inherently good, it would be Sombra... but unless or until the differences between the show and the comic is rectified, he remains an outlier, and difficult to quantify.
For the most part, I believe ponies are meant to be portrayed as inherently good, only acting in an evil manner when circumstances twist them and lead them to behave in a manner that benefits themselves and no one else. However, whether they are truly inherently good, and not merely good only when in better circumstances, is a question that may be more difficult to answer. At the very least when compared to such irredeemable races as the Umbrum it seems to be clear that ponies are meant to be considered good when compared to other species.
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