Actually the Omega Weapon is just a sub-mission boss, you beat them. You level up and get something good. I think the best Ultimate Weapon I will ever fought is the "Ultimate Weapon" in Final Fantasy 7. You have to beat him twice, baby. After you beat him, you get an "Ultimate Weapon" for Cloud, and you can access to the mountain and get the Summon Monster- "Typhoon".
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Ultimate Weapon: 9999 one hit, equip with hit-all...damn...

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First Step: Find your cousin.
Second Step: Get your cousin in the cannon.
Third Step: Find another cousin.
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