I did not understand this movie

I understood who did it and why, and I even figured it out fairly early who it was. But I couldn't make sense of the ending, and I wasn't sure if Katrine was killed or if he just took her finger, and she'd been drugged and wasn't awake when Harry found her or what. And if he (the killer) was doing all of it, does that mean he was the same one who killed Val Kilmer's character and that doctor guy, or was that the other guy, the one J.K. Simmons played?

And when Harry said to him near the end, "It wasn't your mother who didn't want you; it was your father." Then they showed the father watching her sink into the water. So was the father somehow responsible for her doing that, or else why would he said it wasn't her, meaning, we assume, that she didn't purposely leave her son? Ugh, I haven't read the book, so I don't have anything for comparison, but it looked like it would be good, and I love Michael Fassbender, but the whole thing was just so weird to me and didn't all make sense.

Also, what was wrong with Val Kilmer? Does he really look that bad, or was he made to look like that for the movie? He didn't look like himself at all to me, and the voice was so weird.