Board Thread:Questions and Answers/@comment-98.28.168.182-20130418020702/@comment-1210805-20130418032637

Because only the Patriots knew he wasn't dead. Everyone else, including Liquid and all his henchmen, thought Snake succeeded in killing Big Boss in Zanzibar Land. Big Boss was in a nano machine induced coma with a badly damaged body. When you see him in MGS4 his body has been repaired using parts from Liquid and Solidus (hence Solidus' body has no skin or limbs).