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Also, can you increase the magic and physical defense so that it takes a lot of hits to kill it?
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yes, considering that you can pretty much raise it so that the enemy's invincible (hi Guardian)
You can raise it pretty high, but the atma weapon sword, most blitzes, most tools,meteor,flare, and ultima pierce defense and do the same damage no matter what. I have it set up so that only atma weapon and meteor can damage Omega right now, if you use any of the others he throws a temper tantrum and wipes out your party:mog:
Also, 65535 is the max HP, but you can "raise" that significantly by allowing the monster to cast cure 3 on itself in response to every attack.
With quick + life 3 + gem box + economizer at your disposal, I really can't hold anything back at all and still make the boss a challenge.
On a side note, Guardian actually has fairly low defenses, but there is a special line in his attack script that actually makes him invincible. If you don't believe me then you can cast drain on guardian. You still regain health(indicating that damage has been done) but the damage is blocked and registers as 0.