You always use scathe or do you have anyone actually manually attack them.
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Once he loses 2/3 of his health he activates a physical paling rendering Physical attacks and Quickenings useless against him. It drops for maybe a second before he reacitvates it so basically you're stuck using magic against him. Scathe is your best choice cause it's powerful and it has a faster recovery time than Flare. Even then, he activates a magick paling as well but he doesn't keep it up like the physical paling. This combined with his Darkja attacks ability to instant kill is what makes Zodiark a pain in the ass to beat. Especially since death means you have to backtrack through his little dungeon...:mad:
I got Zodiark before the best magics (eg Scathe, Flare) were available.
Zodiark casts paling when his health reaches 20% so right before that I did a quickening and got off a decent chunk of his health. Then I gave all my characters either mirror mail or ruby ring so they all had reflect, and I cast Bio off of them which hit Zodiark 3x. I also had one of my guys casting reverse and decoy so that the other party members weren't affected by his scathe bombardment. Finally, I made sure that my characters all had shell on them to decrease the chances of Darkja from instant KO'ing my guys (if there wasn't time to cast shell I just gave them shell shields).
It definitely would have been easier to wait till after Pharos, but I really wanted to get Zodiark as soon as I could get him.