The purpose of Blackened Skies is to create a new Junko Enoshima in the form of Kaede Akamatsu.
None of the participants are who they believe themselves to be.
Memories are malleable, especially when Flashback Lights are involved. Rather than being brought Back from the Dead, Kaede and the rest of the passengers have been given Fake Memories, convinced that they are the former blackened from their respective games, and pitted against each other.This may be tied into the above WMG; the culprits' endgame could be to prove that this sort of full-scale 'reprogramming' is possible and create their own Junko. Kaede's 'extra memories' of Junko may have also been implanted for the entertainment value — the whole thing may be staged for an in-universe audience who appreciates that sort of 'shocking twist'. Or, if set in a universe where the events of the Hope's Peak series aren't fictional, this could be another one of Junko's contingencies coming into play.
The mysterious investigator is none other then Makoto Naegi
Think about it. He personally ensured there would never be another killing game. So of course he wouldn't believe the rumors. And he also knows that Junko would make sure that the whole world knew there was another one, complete with former killers. And he could have picked up the investigative skills from Kyoko.