Well there is the very real possibility that this was a back-up plan in case Junpei failed.
But that's impossible, as Akane used the Morphogenetic Field to give the correct "way" to Junpie, Thus eliminating the reason for a backup plan.
QUOTE said:
Zero could have found people similar to those that were on the Gigantic when she was there, either in personality, appearance, or both, and placed them on the Gigantic. For whatever reason they were placed on the Gigantic, back-ups or not, this would explain the All-ice like character in the 999 true ending. At the very least, the Allice like character in this game escaped the Gigantic and made it back to land, and looked for a ride back, which was Junpei and the gang.
I don't find the "All-Ice" thing plausable at all, cause if Building Q is in Arazona, even if they were on the Gigantic in the Pacific, there wouldn't really be a reason for Allice to be just casually strolling through the desert after narrowly escaping death.
QUOTE
Going back to the possibility that they were a back-up plan, this would explain the safe ending and how Zero had the ability to put Junpei to sleep, it's very possible that Zero isn't exactly the same Akane as the Akane from the past where Junpei and Akane worked together to save her, but rather an alternate Akane created from the group from this game transmitting their actions to the previous characters on the Gigantic years before, and due to their actions this different Akane chose to become Zero.