Board Thread:General Discussion/@comment-79.52.61.188-20130415085048/@comment-4913740-20130415124738

It's entirely possible that after such a long time, Boss' old comrades no longer recognised him. If I recall correctly, he's looking pretty old by Metal Gear. He could've easily passed himself off as someone else, used an alias.

Or it could be that he acted like he had rejoined the Patriots and was working with Zero again, all the while trying to build his army to prepare for an uprising.