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Depending on where you hit a checkpoint, you might still be able to progress.  The shotgun can open up some new passageways (the green netting).  If you post a screenshot of where you got stuck I might be able to help you out further.  


The green netting was the piece I was missing. Thanks so much for the reply! Just finished up playing through and it was pretty dang enjoyable. I enjoyed how you structured the world with everything being in the same "level", but wrapping around in different ways after you unlock the different weapons.