Hm, the more I think about D2, the more I dont understand why the murder structure mirrors D1s. Nagito even comments on this and uses it to predict 2-4s murder, yet it turns out theres no force motivating them to be similar. Was it just a big coincidence?
I have a personal theory on this based on the whole Nagito "Naegi Makoto Da" anagram and other character similarities that DR2 was originally going to be a straight up MGS2 twist on the first game but was rewritten/toned down at some point. As it stands the best explanation is just the influence of the Junko AI, but that can only explain so much.
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