So I found Zygarde, but all I had were Pokeballs and Luxury balls, so I ran away to get Ultra and Dusk balls. After I ran away, my game said he faded into the shadows... Do I have to defeat the Elite Four like if I had knocked him out? Or will he be back next time I go into Terminus Cave? Please help!
He will return after every time you beat the E4. I fainted it and I returned after I beat the E4 again.
Source: Exp points(experience)
He will return after you beat the Elite Four as if you knocked it out.