The torture scenes aren't the disturbing part. The fact that someone wrote about such innocent characters performing in them is what's disturbing.
Meet Cheerilee: teacher, lovable cartoon character, and - according to fanfiction writer Unahim - a sadistic killer of children. Well, at least the children she deems worthless. Along with those she holds responsible.Cheerilee is facing a problem that probably many teachers have in their careers. Her students are acting up and not paying attention in class, and whatever they do pay attention to just isn't sinking in. Cheerilee has tried and tried again to teach this restless bunch, but everything she's tried so far has failed. Cheerilee is at her wits' end. She feels worthless as a teacher and, thanks to her students' inability to learn, is on the verge of a mid-life crisis. Her whole life, sanity included, is crumbling. She doesn't reach out for help from fellow teachers, nor does she see a therapist. She finds a different, not much better solution.Brutally and sadistically torture and kill any and all children that are giving her trouble, in a way that is very reminiscent of Cupcakes. In fact, many would say Cheerilee's Garden is Cupcakes's Spiritual Successor. Right down to being a Troll Fic gone a little too far.The fanfiction can be read here but be warned: It's Cupcakes's Spiritual Successor for a reason.
:The Bad Guy Wins: Cheerilee has a terrible inability to get rid of evidence in a smart and safe manner. Fortunately for her, Twilight arrives on the scene and unwittingly destroys the evidence for her. Although Cheerilee is killed by Twilight, she gets off scott free while Twilight is blamed for her atrocities.
Descending Ceiling: Scootaloo's "punishment". She's trapped in a metal cage with thin bars for the floor, and a metal plate is slowly descended upon her, eventually crushing her into goo.
Despair Event Horizon: Apple Bloom, though obviously terrified and in mortal agony, stays spirited and defiant throughout most of her torture. It's only when Cheerilee cuts off the skin from her flank and points out that she's failed in her goal as a Cutie Mark Crusader that Apple Bloom is finally overcome by tears. She offers no further words or notable resistance in the remaining few minutes of her life.
It's implied that Twilight's death drove Celestia to this, as she decides that any system that would send her student to her death was flawed, and plans on razing Equestria and forming her new, totalitarian Solar Empire.
Twilight too, upon realizing even Celestia didn't believe she was innocent, driving her to throw herself off the roof.
Hope Spot: There's a short section of the narration where Cheerilee laments that the play is too short to allow her to torture Snails to death as she has been doing to his classmates. So she resigns herself to making his death quick and violent rather than drawn out and violent.
There's one where Celestia rescues Twilight from her execution and proposes they run away, but it's shattered almost immediately when she reveals that not even she thinks Twilight is innocent. This drives the latter to jump off the roof to her death.
By extension, the setup for this tragedy is Spike's final moments, wherein he is able to call for Celestia's help by sending a hastily-written letter describing their situation. But that very letter is misinterpreted by the royal court as evidence of Twilight's guilt, and Celestia's presence at the scene of Cheerilee's death provided the means by which Twilight was saved from death, only to be wrongly convicted. Thus, had Spike not sent that letter, Twilight would never have been Driven to Suicide by Celestia's belief in her guilt, and Celestia would never have been driven to doom all of Equestria to an eternity of tyrannical rule under the reign of the Solar Empire.
I Lied: Cheerilee promises to let Diamond Tiara and Silver Spoon go if the former managed to reach the latter. A difficult task, considering that Diamond Tiara's legs had been Stripped to the Bone by acid, but she pulled it off... and then Cheerilee reveals that she lied and dumps acid on them both.
Has this to say later.
Oh Applejack, so honest that you’ve forgotten ponies can lie, have you?
I'm a Humanitarian: Well, Apple Bloom isn't by choice, but Cheerilee tricks her into drinking what's left of Scootaloo.
Cheerilee herself shows some proclivities toward this, given her increasingly frequent habit of tasting her victims' blood.
The same goes for Twilight, who is force-fed the remains of her friends.
Kill 'em All: By the end of Part 2 of "Scarlet Harvest", the Mane Six, Spike, the Cutie Mark Crusaders, Diamond Tiara and Silver Spoon, Snips and Snails, Twist, and Cheerilee herself are all dead.
Knight Templar: Cheerilee initially seems to become this, thinking that the naughty foals and "corruptive" influences like the Mane Six must be purged to bring peace and morality to Ponyville. Its subversion becomes increasingly obvious as the story goes on, though, culminating in the moment where Twilight calls out Cheerilee for using her "cause" as a weak excuse to cover up the fact that she is a Serial Killer who murders ponies for the enjoyment of it.
Mercy Kill: Cheerilee made an already-tortured Rainbow Dash do this to her friend after mortally wounding her..
Never Say "Die": Believe it or not, played straight at the end of Diamond Tiara's and Silver Spoon's torture.
“Both of the fillies looked up as they heard a rumbling noise coming from a pipe above them, and as they saw a familiar clear liquid gush down they realized they wouldn’t get to see anything else, ever again.”
Sadistic Choice: Silver Spoon is given one in the form of a button that she can press to temporarily stop her torture device, but pours acid into Diamond Tiara's trap.