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Screw the spoiler tags. I read somewhere that Walter and William Bell always had intentions to experiments with cross-over, which is true given that they experimented with kids even before Peter of this world died and Walter crossed over to grab the other Peter. So even if Peter never existed, these two found a way to cross over and caused the first wormhole on their side and one thing led to another causing the fighting.
Also remember that scene in the future between Peter and Walter discussing about the consequences of cheating time? I think Peter went back in time to 2 worlds that never had Peter.
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