It seems Cheerilee couldn't protect Sweetie Belle. It seems that now this filly will not have the best fate...

---SOME BORING LORE DIALOG---

ATP: So, MAG-41, did you bring a sample of the unicorn?

MAG: that thing?

ATP: Exactly, great job!

Scientist: So, now we need to take it to the “magic overload” experiment in this test chamber. Assistant, please.

The assistant silently roughly tied the filly by the neck, chest, and forelimbs. The MAG agent lowered her to the ground. Assistant handed over the resulting “Leash to the scientist.”

Scientist: Great, let's go.

The Scientist and the Assistant went into the test chamber, taking the filly. And I think even “Cupcakes” is not even close to the following events.