Board Thread:Questions and Answers/@comment-5414293-20130624031632/@comment-1971498-20130624094635

Crony wrote: He fought him to test him, simple as that. He wanted to see if he was worthy of the title "Snake", and was true to the legend that Big Boss was. If Snake was to fail against Ocelot this day, well that would mean the Patriots' plan was not going to succeed anyway.

This is pretty much the most plausible answer. Ocelot always found different ways to make his plan work while joining in the fray to have some fun of his own. Heck he was meant to help and protect Big Boss in MGS3 as ADAM, and look what the hell he was up to in that one.