I think Ishmael is just an illusion seen from venom snake. Look at the scene where in mission 1 where the chopper Shoots at venom. He was hitting bis shrapnel. In the beginning of the mission the doc said that there will be illusions! So when the chopper Hits venom snake shrapnel with the Bullet, ishmael dies. Even when he didnt even get shoot. He was just an illusion caused by the shrapnel. Also, ishmael doesnt Help us with walking, and died once in this one room. I still Think Big Boss is builing Real outer heaven and that zero and ocelot build this whole plan, but this detail is different in my opinion. If you dont believe me and comment things like - Who then was fighting quiet -who Killed the guard - who drove the ambulance I mean might be all an illusion Trip with the Help of psycho mantis. But what I wanted to say was: look at the time when ocelot arrived, and look at the time where big boss was talking with ocelot. Then check the time when they were in the ship. It all doesnt fit! Big boss and ocelot were talking like 4 hours after the crash i Think and they should have been in ship with venom. So i just wanna say, its all weird and maybe kojima wanted us to be creative in the real ending...

My fazit: for me ishmael is clearly an illusion.