[MASSIVE SPOILER THREAD] The end

[thepaleking]

As Fonzo said, there is no "good" or "bad" ending. It all depends on what your feelings are toward Daniel, Alexander, Agrippa.
One can see Alexander as evil, simply because he tortured and killed so many people; another person can see his actions as just, because he was a higher form of life than normal humans, and was trying to return home after being unwillingly trapped on earth.
Daniel is not a "good guy" in the way most game protagonists are, because he did in fact torture and kill people, including a young girl, all in an effort to save his own skin. However he was in way coaxed into doing so by Alexander, who in turn betrayed him by using him as bait for The Shadow.
Even Agrippa, who seems fairly innocent, did at one point, I believe, betray Alexander by taking his place in the portal ritual.

So yeah, the endings are just different, none are better or worse.