I feel like a lot of people just ignore Tokyo Soul season 2, which sucks because it was actually pretty good. And has some interesting lore implications.
In it, it's revealed that Sam has amnesia and is living in some sort of "fake world" held within the wasteland remnants of the original Tokyo Soul. When escaping with some scientists, an older Jerry who is trying to free Sam (to avoid using the Taurtis skin) and DoughBoi, they get captured by Wastelanders, and their leader is revealed to have the Necronomicon, who recognizes Sam.
Sam, despite having amnesia, immediately recognizes the Necronomicon and even calls out that he and the cursed book are supposed to be on good terms. It's as if seeing this book that helped him fulfill his destiny to destroy the universe unlocked his true memory, and perhaps his true personality.
Throughout Tokyo Soul season 2, while having some questionable moments, Sam is generally a good guy. He even questions why Jerry and Doughboi were his friends upon learning how terrible he used to be. Ultimately, Sam with amnesia is a lot like Sam from the first few episodes of YHS Classic.
But upon seeing and interaction with the Necronomicon, he suddenly shifts. While saying he does not want to kill one of the men he's working with despite facing death, he has absolutely no reservations in pushing the man into a death pit even after the man gives up.
At the end of the finale, Sam Jerry and Doughboi get the Necronomicon back from the wastelanders and use it to essentially wish for a new reality to be transported to (Well, Jerry makes the wish to go back to old times).
While the following series was a sorta YHS Reboot, it is definitely not canon as it isn't in the official playlist, unlike the current reboot and TSs2. So it is heavily implied that the current YHS Reboot is the new timeline, or possibly one of the many new timlines, as we don't know how long Sam has been doing this sorta thing since he got his memories back. With Jerry not being a part of the main series, it is easy to speculate that Sam is in full possession of the Necronomicon.
One other thing that Tokyo Soul season 2 does is help prove that Sam doesn't have amnesia in the Reboot and is simply acting oblivious at times. We know Sam is a kinder person with amnesia, yet Reboot Sam is very much worse than YHS Classic Sam and Tokyo Soul Sam.
I think the only question this leaves is why are elements from YHS Classic showing up in the Reboot. Well, I think it's because the more Sam destroys and recreates the timeline, the thinner the walls between realities become. So, due to all his meddling, Sam's past is starting to catch up to him.
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