"Nobody is going to bother you where you're going..." Isaac teleports Chrono to a Subjugator Indoctrination camp, where his past self is erased and new programing is forced upon him. He would soon be slated for training as a Heinrich Himmler-Class Immolationist, and would quickly rise through the ranks, passing Exterminatist, Genocidist, Holocaustist and finally making Extinctionist.
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Eh heh heh, Dark Side ending...