Penumbra overall storyline and a few questions?

[Ssschah]

Who was the shadowy figure at the end of Penumbra Overture? Because I know you walk into that final hall and see a person standing there, then when you start to walk towards him or rather it the lights turn off and a tuuringait(?) hits you unconcious and you wake up in a room they were using for cells? Also how come they took you prisoner if later in the game overtime they see you they want to kill you? And at the end they don't want to kill you? So much confusion and so many questions...