Deadliest of the species confusion

Ok, I recently got the AvP Omnibus vol. 2. The first story in there is Deadliest of the Species. I LOVED the way it started out. My enjoyment lasted a little past the half-way point, and then everything stopped making sense.

I'm sure there was a deep, emotional ending in there somewhere, but it was lost on me.

There has got to be something I'm missing here. This is supposed to be one of the best AvP comics ever, but I just didn't understand the second half at all.

And no, it's not beyond my reading level or anything. I read "From Hell" (the graphic novel, not the actual letter) with no problems, but an AvP comic is giving me trouble... It's kind of frustrating.

I was just wondering if someone could please explain in simple terms what the hell happened in the last half? About after Caryn is kidnapped is where it got weird.