The game's story is thread-bare and incomprehensible in places because a bunch of stuff got cut extremely late to get the game out the door. The entire Zack thing. Yuffie and Vincent had almost everything related to them cut out entirely. And then there was the english localization which fixed some of those issues but added more of its own with the pretty bad translation making things even harder to figure out. Square would end up doing the same thing but far far worse with Xenogears with large chunks of the game removed and replaced with text at the beginning of the second disc to give one example.