[SPOILER] Plot Discussion Thread *Spoiler Alert*

[aquilantiqua]

Hallucination/mental play - my favorite. Mandus builds a Machine on the bones of his children, he himself becomes part of the Machine, a machine itself, lying in the sarcophagus. His personality splits on two - The Machine and Mandus. Since he is the heart of damned device, each time when these personalities clash they cause havok to actual machine: Mandus wins at some point, "sabotaging' device and shutting it down. The Machine manages to shoo him, but in order to restore device it needs Mandus. So it "wakes" him up, and with trickery get his help in restoring "power" again (I assume the consciousness of his body in the lung can somehow operate machine). Second personality, ie Mandus. realizes it and he fights Machine again. Remember how he talks about making himself "whole again"? In the end I think Mandus wins, he accepts the truth, what he did, he accepts his damnation and thus completely takes over the machine (1st personality), becomes whole again and shuts down The Doom's Device since nothing can prevent him to do so anymore.
Now, what is about what we see in-game, all the locations and actions we do? This is the brain's interpretation of the clash of the personalities that happens in his mind. The notes we find is the memories his 2nd personality uncovers, it is all in his head. Pigs are obstacles, but that does not mean they don't exist in outer world, they do.

The ending makes absolute sense if you frame the story this way too. It would mean the whole end scene which ends with him plucking his own heart out is a representation of his sane half winning, taking control of the facility, and possibly destroying the heart we see at the center of the machine. If that were true, it would answer why killing himself kills the machine.