Prologue
Rainbow Dash, Rarity, Applejack, Pinkie Pie, Twilight Sparkle, and Fluttershy crouched panting in front of Queen Chrysalis.
“Although, I have to say I have thoroughly enjoyed this quarrel,” Chrysalis applauded with barely distinguishable mockery, "but I have to go." Chrysalis turned around her crooked glowing with magic
Suddenly Fluttershy felt a sudden urge come over her.
“No!” Fluttershy shouted and flew forward into Chrysalis’ back causing her spell to go off. The rest of the Mane Six could only stare in horror as Fluttershy and Chrysalis were enveloped with a sphere of magic.
“Fluttershy!” called the Mane Six; Rainbow Dash charged forward as Fluttershy and Chrysalis began to fade only to pass through.
“Fluttershy!” Rainbow Dash called at the area the yellow Pegasus had been, no answer. Rainbow Dash turned to Twilight “what happened.” Twilight glanced from the area to Rainbow Dash, but could only shrug helplessly.
“How can you just shrug,” Rainbow Dash demanded.
“I don’t know,” Twilight explained.
“You don’t know. You don’t know!” Rainbow Dash demanded, stomping toward Twilight her sorrow turning into rage.
“Hold it, Rainbow, yellin’ won’t help here,” Applejack intercepted, pulling Rainbow Dash back by her tail, though she couldn’t really blame Rainbow Dash for her sudden outburst. Losing Fluttershy was a crushing blow to all of them, but would be even more so for Rainbow Dash. Anypony knew that Rainbow Dash and Fluttershy were pffs (pony friends forever) long before coming to Ponyville.
Hello!
From what I can tell from the Prologue, you seem to be missing a bit of punctuation.
This sentence was a bit awkward to read since it was lacking commas. What you have here is a complex sentence, and it would run much smoother with commas inserted into the right places. Your wording is a bit awkward as well. The sentence just doesn't sound right when spoken out loud. I would rewrite it like this:
"Although I've thoroughly enjoyed our little quarrel, I'm afraid I have to go," Chrysalis applauded the six ponies with barely disguised mockery. Without waiting for an answer, the Changeling Queen turned around, her crooked horn glowing with magic."
I know it seems pretty drastic, but using different words and punctuation can make a big difference. Try being more vivid with your descriptions, throw me a bone, make me feel as if I'm right there with the ponies!
I hope this helped!
Also, if you've any more questions, don't hesitate to shoot me a message!
EDIT: Aha, perhaps I should take my own advice! I had a few spelling mistakes myself. Oops!