You can start the side-quest to get every ultimate weapons for your party members after the events in Abel's Ark (DISC 2)
Shion - Miyuki Special
To obtain this weapon walk by the UMN "machine" at the Elsa (near the saving point, the shop and the EVS; Again this must done after the events in Abel's Ark)and Miyuki will contact you and offer you to make Shion's ultimate weapon, but she needs a geocrystal from you. The rough geocrystal is acquired on the floating landmass by destroying the giant purple crystal. If you don't have it, go back to the floating landmass using the EVS.
Go to the UMN "machine" again, she'll tell you that you have a rough crystal, but she needs a pure one, so go to the women's quarters and have Bunnie refine it for you. Go back to the UMN "machine" and Shion's ultimate weapon Miyuki Special is all yours!
KOS-MOS - KWP-XX
Getting KOS-MOS's ultimate weapon is quite simple, but expensive
After the events in Abel's Ark, this weapon will appear in the online store, but you'll need 300,000G to buy it.
chaos - God Breath
Talk to the droid in the bar inside of the Elsa , who is obsessed with a stone, he will tell you that you need to return to Abel's Ark, once you are there go back to each of the spheres you previously entered.
Head for the rooms where Zohar emulators were spinning in each of the spheres, there you'll find a shinning light, examine it.After getting all four of them, go to the "core"( the room the spheres are rotating around) and you will receive "God's Breath" and an item called "The Universe"
Jr - Vaquero
In order to get this weapon you must finish the fifth world of Hakox (a game that is located inside the bar of the Elsa)
I wish you good luck with this one, you'll need it.
In my opinion, this is the hardest ultimate weapon to obtain.
Ziggy - Gnosis Nail
Talk to CABRILLO, the android near the E.S. elevator on the first floor of the Elsa, he'll say he will make Ziggy his final weapon the Gnosis Nail. But in exchange you'll need to collect 99 Sephirotic canes!
They are found only on Azazel and Armaros Gnosis which are only found in the final two maps of the game.
Just stay around a save point and keep fighting
those Gnosis, reset the map when needed (to make them re-appear).
While this isn't hard, it is really tedious, so only people with patience and free time should do it.
MOMO - Moon Bridge
Go into the women's quarters on the Elsa and talk with KAMIKAZE. The droid will tell you that
the Elsa's pet Alby has gone missing into the Durandal through EVS.
Go there and talk to the dog at the docks.
It will run off and operate the transport train in the Durandel. Head to the park and go up the escalator to see another scene with the dog.
Then enter the park and head for the right side to see the finally receive the weapon Heaven's Door.
Then head back for the Elsa and speak with KAMIKAZE one more time to receive the Mood Bridge and finally speak with VALENCIA (another droid) in the Elsa's E.S. Hanger to use Heaven's Door.
Jin - VB-Dawn
In the men's quarters bathroom of the Elsa is a droid called PANACHE, he will tell you that he is learning how to make a legendary sword. But he needs some ingredients:
1)Buy a weapon called the VB-Crimson and make sure to leave it unequipped.
2)Next is a special Item called the Prayer Beads.
To get it walk around the world map of Miltia, it's on the right side, there is a district that is locked, use the code 5150 on the door and the district will now be unlocked, there you will receive the Prayer Beads.
With both of these items PANACHE will forge the legendary sword VB-Dawn and you will also receive an accessory called Nine Stones.