So after beating the game I've finally compiled all of my thoughts and analysis regarding the storu into one blog:

http://www.gamespot.com/users/mgsfan104/show_blog_entry.php?topic_id=m-100-26031354

It's a bit long, so enjoy if you like. I'm pretty sure that I forgot to include some stuff so I'll probably end up adding to it later, but for now I think its got most of my thoughts down. Also, SPOILERS!

This is my entry for the writing contest, some feedback would be nice and if you find any erros please let me know:

http://www.gamespot.com/users/mgsfan104/show_blog_entry.php?topic_id=m-100-26018081