This was a crazy fic about Twilight and Rainbow dash taking care of Fluttershy's animals, only to be ambushed by a ninja clan who nearly takes them out.
That is until Fluttershy comes to the rescue.

And the culprit behind the clan was Rarity!
I told you was crazy!

But like I said, I have been trying to rediscover this fanfiction, but it has been elusive to me so far.

It had this picture:

https://images-wixmp-ed30a86b8c4ca887773594c2.wixmp.com/intermediary/f/f9c111ae-c304-4507-a071-13c9c089877e/d4l9e02-2a7f3927-f379-470f-99ee-a9cf12767e3c.jpg/v1/fill/w_900,h_720,q_70,strp/ninja_fluttershy_by_swomswom_d4l9e02-fullview.jpg