There's a darker side to harmony...
The Elements of Harmony. For generations these ancient artifacts have served as the physical manifestations of Equestria's most important principles: Loyalty, honesty, generosity, kindness, laughter, and the magic of friendship itself. However, only specific ponies are capable of harnessing the Elements' power and little information on them exists in Equestrian literature. And many questions remain unanswered, but there is one above all else: what qualities, spiritual or biological, are needed to allow a pony to control the artifacts representing the Elements that protect the world, and thus assure that the world is not destroyed by the seeds of chaos? What does it take to keep harmony secure?
Twilight Sparkle doesn't know, but she intends to find out by creating her own research on the Elements and their bearers in order to achieve her own Well-Intentioned Extremist goals. But how far will she go to preserve harmony and protect the future, and how will the fate of her friends play into it?
Research, procedures from the pits of Tartarus, and a "harmonious plan" that promises to bring about a new world, that's what.
Started on July 25, 2012, by Shadowed Rainbow, Pages of Harmony is a grimdark My Little Pony: Friendship Is Magic fanfic and contains extremely graphic content. The story itself can be read here 
or here, a reading is here, and a short movie trailer can also be found here . But BE WARNED you'd better know what you're getting into.
Also had a series of text-based Ask a Pony blogs: Twilight herself (done by the author, no longer active), some of Twilight's followers (deleted), some of Twilight's opposers (inactive), and Fluttershy (deleted). Be warned, though they are AU to the main fic, it takes place after Chapter 12, so expect MAJOR spoilers if you haven't gotten to that point.
Has been completed as of October 2014. An attempt at a sequel, Empress of Harmony was made, but never made it past one chapter.
As of 2018 it's getting a Continuity Reboot due to the original being an Old Shame.
Pages of Harmony contains examples of:
- Afterlife Antechamber: The bearers of the Elements that Twilight kills end up being sent here, able to communicate with Twilight when they directly speak to her.
- And I Must Scream: Rainbow Dash would like nothing other than to be able to kill Twilight, but seeing as she can't interact with her as a spirit, it only serves to make her angrier.
- Ax-Crazy: Twilight Sparkle. And Rainbow Dash after her Mind Rape.
- This happens to Apple Bloom as well, right before she discovers that Applejack is missing.
- The Bad Guy Wins
- Berserk Button: Never suggest to Twilight that what she's doing is like Discord, or she'll attempt to attack you even if you're a manifestation of her conscience visible only to her.
- Big "SHUT UP!": Twilight shouts this at her conscience-self after the insistence that what she's doing is wrong.
- Body Horror: When Twilight becomes Harmony Incarnate in chapter 12
- Break the Cutie: It's been stated that Fluttershy gets the worst of Twilight's experiments because her Element is the hardest to break. Also, for a more meta reason, because Fluttershy getting hurt is generally considered the fandom's collective weakness.
- Chronic Backstabbing Disorder: Twilight herself betrays all of her friends, one by one.
- Cold-Blooded Torture: No, really?
- The Conscience: Rather than being a specific other character that is this in a narrative sense, Twilight's literal conscience manifests as another version of herself, who retains Twilight's normal appearence despite the Madness Makeover and Sanity Slippage that the real Twilight progressively goes through, attempting (and failing) to act as a Morality Chain
- Darker and Edgier: As of chapter 10, the story seems to be headed this way. No, really. What seemingly started out as a simple gorefic in the vein of Cupcakes (Sergeant Sprinkles) is now revealed to be a story about Twilight Sparkle trying to Take Over the World (or rather, the universe) and commit genocide on any living thing without the capacity for the Elements of Harmony. The worst part of that is she denies that her plan is morally wrong and refers to it as "cleansing" and being for the good of harmony.
- The sequel looks like it's going to be headed in this direction in comparison to its predecessor, despite the lower rating. That "cleansing" for the good of harmony? We're going to see it all happen.
- Dark Fic: The whole. Entire. THING. As said by one person on dA, it "makes Cupcakes look like Barney".
- Enemy Within: Subversion - Twilight sees her conscience as this, seeing it as an interference in her plan, even though her conscience is in fact attempting to steer her back on the right path.
- Elaborate Underground Base: Twilight's laboratory underneath her library is definitely this. As of Chapter 10, we see the contents of two rooms (one being her main laboratory work area), but there are many other doors down there that the reader has no idea what's in them at this point, or how far it goes.
- Electric Torture: Used on Applejack as a form of conditioning to make her lie and thus lose her Element.It also gets used briefly on Rainbow Dash earlier in the story as a method of shattering her loyalty.
- Evil Counterpart: Inverted. Twilight, the Villain Protagonist, is introduced first, while her mirror-image conscience begins to show up around Chapter 4, trying to get her to see the error of her ways.
- Evilutionary Biologist: Guess
- Eye Scream: When Twilight tortures Sweetie Belle and then brainwashes Rarity into killing the little filly. Fluttershy also gets a hot plate pressed against her eye as part of the procedure to extract her Element.
- Flaying Alive: Done to each one of the other Element-bearers in the form of scalping, but done in a more complete sense to Spike.
- For Science!: Twilight uses this to justify what she's doing, claiming her experiments are necessary to strengthen Equestria's defense mechanism of friendship and harmony.
- Freudian Excuse: Rainbow Dash is the most evident example. After Twilight uses mental manipulation on her to rewrite her memories and destroy any sense of loyalty, and she dies soon after, she swears to get revenge on Twilight by getting her to die and burn in Tartarus for all eternity.
- From Bad to Worse: Thought Twilight just wanted to isolate the elements from her friends by breaking their spirits, right? Well, turns out she won't be finished until she's wiped out every single organism without the proper genetic traits for harmony.
- Glasgow Grin: Dear GOSH poor Sweetie Belle. The way that Twilight delivers lines right before it only makes it worse:Twilight: Pinkie knows that smiling helps ponies be happy, and it's a fact. (leans closer) Now go on, smile. It'll help you feel better. (after Sweetie Belle doesn't smile) You're not smiling!
- Gorn: Quite a bit of the ENTIRE fanfic. The gore always has a purpose in context however, and the meticulousness of it just makes things worse.
- Grimdark: GRIMDARK AS TARTARUS.
- Hope Spot: Rainbow Dash has one after Twilight finishes using a machine to briefly electrocute her. Only for Twilight to reveal she was testing it to make sure it can administer jolts of electricity to Dash's brain properly.
- Human Resources: Twilight separates the body parts of her friends after they die to preserve their bodies as books.
- Hypocrite: Twilight claims that she's ridding Equestria of all evil when all she's doing is actually making things worse.
- Ignored Epiphany: Twilight ignores her conscience after she starts her plans of taking the Elements.
- I'm a Humanitarian: Rainbow Dash as a result of Twilight using her Mind Rape techniques.
- Immortality Seeker: Twilight plans to become immortal after instituting her new world order, simply because she's afraid her successors won't use the same methods.
- Madness Makeover: As the fic progresses, Twilight goes from her normal-looking self to a disheveled-looking, pinprick-eyed Laughing Mad mare.
- Mad Scientist: Twilight Sparkle, to the extent of experimenting on her friends to extract their Elements. And it's implied with her talk of purity that her plan goes beyond that... which is eventually confirmed
- Mad Scientist Laboratory: Twilight has one directly below her library which she uses to perform her research.
- Mind Rape: Happens multiple times, each with its own horrifying twist.
- Multiversal Conqueror: Twilight aspires to be this - though she'd prefer to use the word "Cleanser", as she sees her actions as being for the greater good.
- A Nazi by Any Other Name: Twilight. After she figures out what the genetic component for the Elements of Harmony is, her plan is to commit total genocide on anything without those genes, in a matter suspiciously (and deliberately) similar to the Holocaust. On a universal level. And, if it exists, the multiverse.
- Necessarily Evil: Twilight genuinely believes that killing her friends, extracting their Elements from them, and killing off everything without the potential to exhibit them will destroy chaos and allow harmony to reign.
- Omnicidal Maniac: Rainbow Dash actually refers to Twilight as this in chapter 10, although technically Twilight doesn't want to destroy everything - just everything without the right genes for the Elements. Then again, Rainbow Dash tries to refer to Twilight in any negative light she can, whether it's true or not.
- Plagued by Nightmares: Twilight begins suffering from them after killing Rainbow Dash, beginning the cycle of communicating with her other victims as they're killed.
- Playing with Syringes: Twilight Sparkle, and each of them does something completely different.
- Red Oni, Blue Oni: Rainbow Dash is the red to Twilight's blue, though the character alignment is subverted with Twilight being the more villainous of the two.
- Sanity Slippage: Twilight's sanity starts to noticeably decline as the story progresses.
- Schizo Tech: Twilight's hidden laboratory.
- Shout-Out: During Rainbow Dash's Mind Rape torture, the story slightly mentions both Rainbow Factory and Cupcakes (Sergeant Sprinkles), two other well-known gorefics. While Cupcakes is only slightly alluded to with Pinkie in one of Rainbow's Mind Rape visions threatening to hack her wings off, the Rainbow Factory mention is quite blatant... and it makes everything much worse.
- In a non-MLP example, Pinkie's gesture language and Rainbow Dash's interpretation of it is an reference to Haroun and the Sea Of Stories, when Mudra the Shadow Warrior communicates to the Storyteller Rashid in this manner.
- When she presents Applejack with Spike's mutilated body, Twilight comments, "He's met with a terrible fate, hasn't he? It didn't have to be like this. He didn't have to die..."
- Shown Their Work: The amount of research put into this fic is astonishing. To elaborate it describes actual scientific procedures and forms of torture, among other things.
- Slasher Smile: Twilight has one and it's always present during one of her experiments.
- Spider-Sense: Pinkie's "Pinkie Sense" makes an appearance when her pinchy knee tries to signify something scary's going on. Unfortunately, by the time she's figured out what it is it's too late for Rainbow Dash... and her.
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Spiritual Successor: Possibly to The Experiments of Twilight Sparkle, albeit a more thought out and darker one. - Strapped to an Operating Table: Twilight restrains her friends in this manner so she can experiment on them and remove their Elements.
- Sufficiently Analyzed Magic: Everything having to do with Twilight's Element-Analysis.
- Talking in Your Dreams: The ponies that Twilight takes their Elements from communicate with her in this way.
- Take Over the World: Twilight's plan as of Chapter 10. And it goes even further than that.
- 2 + Torture = 5: Twilight does this to Applejack. Complete with 1984-esque Electric Torture.
- Villain Protagonist: Twilight, obviously. Rainbow Dash is a secondary example of this.
- The Voiceless: Pinkie forcibly becomes this when she has her larynx ripped out.
- Well-Intentioned Extremist: Twilight's goal to preserve harmony in Equestria is admirable. Unfortunately her methods are anything but admirable.
- Wham Episode: Chapter 10. Suffice to say, Twilight's plan isn't what it seems from the early chapters. It's ten times worse.
- Would Hurt a Child:Two of the characters that have been killed by Twilight have been Sweetie Belle and Spike. Not because they were essential to Twilight's plan, but because Twilight thought they posed a potential threat to her.
