The plot of Inner Demons is driven by a prophecy that Twilight Sparkle will succumb to the darkness in her heart and become the "Queen of Darkness", who will take over all of Equestria. This happens within half a dozen chapters, and Queen!Twilight proceeds to take up the mantle of Big Bad for the story.
Trixie starts out the story as The Atoner, who wants to learn true magic from Twilight in order to make up for her boastful and arrogant past. When Twilight turns, she talks Trixie into helping strike at the other Elements of Harmony... then Trixie sees how powerful Twilight is, and performs a full turn herself in order to convince Twilight to keep her.
In a rather Shocking Swerve, Sweetie Belle and Scootaloo, who join up due to a combo of More than Mind Control and not seeming to be fully aware of what's happening.
In the Pony POV Series, Fluttershy suffers a severe Break the Cutie and falls victim to the same corruption as Nightmare Moon, transforming into the Big Bad of the story arc, Princess Gaia/Nightmare Whisper.
There's also the Dark World versions of the Discorded Mane Six, who Discord uses as his Co-Dragons for a thousand years until Cadence's spirit helps Twilight remember her true self, beginning the eventual Heel Face Turns of all of them.
The Nameless Passenger turns out to be a version of Twilight who turned into a vengeance crazedNightmare seeking to punish Discord for all eternity via Groundhog Day Loop, no matter how many lives she may ruin or erase in the process.
Horseshoes and Hand Grenades has Gentaro do one when Kengo didn't revive him. A being known as Ophiuchus resurrected him and brainwashed him to believe that his friends wanted him to die and left him to the hands of Ryusei Sakuta/Kamen Rider meteor. Things get very bad.
