Zoroark was captured by Kodai so that he could use its Illusion ability so that it could transform into the legendary Pokémon Raikou, Entei and Suicune to terrorize the people of Crown City so they had to be evacuated. It is friends with a Zorua that it was trying to protect from Kodai but that friendship ended up being a weakness that Kodai could exploit against it.
Zoroark was almost killed by Kodai but Celebi managed to heal it before it died. With help from Satoshi and his friends, Zoroark was able to return back to its home with Zorua.