The after math:

Rarity was sent to an asylum where she lived insanely, ever after

Twilight got away without anypony noticing, but now she no longer works for the agency.

Applejack lived but has a scar on her throat.

Winona was horribly injured, but she survived.

The SWAT team tracked the messenger on Rarity's watch and found the agency and arrested most of the agents working there, very few escaped.

The mare who messaged Rarity is still unknown, but some think the voice could have belonged to Spitfire, the leader of the wonderbolts.

Opal is only a robot made to receive messeges and capture footage.

No pony knows why the agency wanted Applejack dead.

Author's Note

my first fanfic i've written, finished, and published. I didn't work hard at all and I can't promise there will be better fanfics made by me in the future...