Ok, here goes:

A sight revered, yet with the sound of death,
Found in the darkness, with other's waiting,
One of the few, who doesn't kill with it's breath,
Many who tried, found themselves failing.

The first stanza refers to stealing them from Ultima Weapon in the Omega Ruins.

Not knowing the truth, yet fearing the past,
Yet you you prevail, the trio will help,
But beware, though the enemies death comes fast,
But the strong become weak, just like that little whelp.

This stanza refers to the Trio of 9999 Overdrives making all your character do 9999 damage each attack, thus making the weak strong. And that Omega was banished to the ruins, which you get the wings of discover from him and that forms the mix of trio of 9999.

Sorry for the confusion, I'm still getting used to this place.