In order to avoid upsetting Fluttershy while still creating chaos, Discord traveled to an alternate universe to wreak entertaining havoc, and picked the wrong one.

In the core universe, Spike receives a letter from Discord begging for help, and soon the Mane 6 are preparing to travel to the alternate universe to rescue him from their own twisted counterparts. Meanwhile, Discord struggles to keep his mind and will intact, while the alternate Twilight Sparkle seeks to use him as a source of magical power to be harnessed to Order, and the alternate Fluttershy expresses her own twisted mixture of desire and resentment against him.

There are no explicit, current, healthy pairings. There is the usual Spike/Rarity crush, past Discord/Celestia from long ago, unconsummated/unacknowledged feelings between the real Fluttershy and Discord, and a sick, totally messed-up relationship between the alternate Fluttershy and her prisoner, which I wouldn't even call a pairing since it's rape, except that the thing that makes it especially destructive is the presence of genuine emotions in it.

Graphic torture. Somewhat explicit, non-violent but psychologically destructive rape.