Given that Ruby Weapon attacks using his tentacles, Ultima spells and one move that instantly removes a party member from the game, i think you've gotten them mixed up. Ultimate Weapon flies around the map. You have to deal lots of damage to him in each battle (that you can trigger by ramming him until he stops), then one time he will stop over Cosmo Canyon. This is the last fight with him. I think it's only possible on disc 3. If you still think it's Ruby Weapon you're fighting over Fort Condor, post a screenshot, and we'll see. If it is Ultimate, try hitting him with soemthing that does a lot of damage, like the Bahumut set of summons.
Ruby Weapon appears after you've beaten Ultimate Weapon, then had at least one random encounter on the world map. Emerald Weapon is underwater most of the time, but for some reason doesn't always appear (I guess he might be on the other side of the ocean, so maybe I just can't see him). Information gathered from my PC version, which I've had for about 10 years (only recently reinstalled, but I remember all this).
Heck, maybe you do have to go to Cactuar Island. I always collect three Tetra Elementals from there as soon as I can, so I have no idea if that changes anything else. Worth a try as much as anything.