The SOUL, as a proxy for the player/reader, disconnected out of guilt.
The last several comics displayed the harm caused by the SOUL, from emotionally scarring Kris to terrifying Asriel. The Knight revealing that they/we had been intentionally manipulated into causing the maybe-apocalypse that we see was just the final straw, and the SOUL disconnects from Kris and leaves the story intentionally on a cliffhanger from our perspective.http://tvtropes.org/pmwiki/pmwiki.php/WMG/PaperTrail
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