Metal Gear Solid 2 not making sense?

I enjoyed MGS2, but not all people did. One big reason is it makes absolutely no sense. It felt somewhat... awkward playing it because of this and made objectives really fuzzy.

However, somebody actually spent some time and analyzed the plot in such a way that it might make the game more enjoyable that second, third, or 97th time through.

Link.

Via Kotaku.