I found myself sort of bummed by it at first because I thought the guitar part was pretty, and I was enjoying it and wanted it to go on. But then, I grew to appreciate it. It reminds me of the inscription to the book, "House of Leaves": this is not for you. I don't have Opeth in my pocket. And when I accept that, and sort of follow their lead (or Mike's), I'll get it.
What I get from it is disintegration. It's like a still life of rotten fruit. Not beautiful, but it tells a story. All beauty fades. Innocence is corrupted. Aren't these the kind of themes Watershed is built around?
Furthermore, Fred does a great job of detuning, so that as it falls apart, there are moments where it sounds nearly like it's morphed into some new tonality. Kind of a cool listen if you let yourself go.
Kind of reminiscent of the end of "Friends" on Led Zep III, actually.