[Klashikari]

Yes, actually I was suspecting something, especially due to third case circumstances

Spoiler for Up to chapter 3 theory:

From my understanding, it really seems like Junko is recreating the same situation that occured in DR1, except that instead of having the hope of humanity, she use the despair of humanity.

What struck me important is the timeline: SDR2 students have to be thrown in mutual killing game after DR1 events, but that doesn't mean they were kidnapped after the malefaction and the academy shelter plan were on the move.

We still don't know what happened during that malefaction event, nor "how many" the SHSL despair were, so I'm starting to suspect that it is partial or actually all of them in SDR2, especially because of Mikan's comment "I became like this because of you". Which actually means that they were bad enough to twist Mikan to that extent.
Furthermore, even if they say "this Mikan doesn't exist", it is because she lost her memories from the time she spent in Kibougamine academy, therefore, it is -very- likely it is a "corruption" which is linked to the malefaction back then. Prior that, it is very likely the "Mikan we know" was the original Mikan, before her transfer to Kibougamine.

Finally, Hajime's amnesia is more than suspicious, because unlike Makoto, he has to gain a proper title, due to Nagito's good luck (and I doubt they would wait for the good luck guy to graduate before selecting someone else with the lottery).
If Junko is again trying broadcasting a mutual killing for her despair objective, it would make sense to have a "normal" guy to realize later on he is a damn despair guy incarnate.

And why Junko is still there? She most likely decrypted Alter Ego algorythm back in DR1 and made a copy of herself as an AI. The fact Monokuma reactivated by the end of DR1 is a major giveaway.