A mystery is a foot as new animals suddenly appear at Flutter Shy's home.
The Cute Mark Crusaders decide to solve this mystery on there own, but when they disappear Twilight and Friend head out find them.
Mean while in a town know as Clarksville Noah and her sister Megan are volunteering at the Town Zoo when they are attacked by a Bug-pony. Noah, Megan and there friends Richie and Ella must find their answers at the Clarksville Zoo.
Little does either group realize that answers to what they seek can only found in The Secret Zoo, where our two groups of heroes will meet, along with enemies old and new.