It's not really "random", there is a coherent story (and a moral to that story) underneath all the weirdness and you'll sometimes forget how crazy it's gotten because your current objective tends to make sense (ex: "defuse the bombs").

But all MGS games are basically playable Kojima manifestos with sci-fi trappings. The actual minute-to-minute gameplay for them is really, really good so even if you don't dig the story they're worth playing.

The previous poster is right that MGS4 does clear a lot of this up. But MGS4 also slams more weirdness and callbacks to the previous games on top of it.