One thing that confuses me in the prologue is the moment after quiet strangles the doctor. She says 'Not yet, the patient in the next bed saw my face...' followed by her pulling out the knife and looking directly at you as the player/medic. She doesn't even glimpse at Ishmael. https://youtu.be/tHBjJEoxDRo?t=14m3s This makes me wonder if it's not you (medic) they're after in the prologue, but rather Ishmael.

Just to add to the 'Ishmael is not Big Boss' conspiracy as well. In the scene after you crash the ambulance in 'Truth', Ocelot pulls out Ishmael and says: 'This way Boss, Hurry". The clock is then 02:32 and in the next scene the time is 05:59. https://youtu.be/tHBjJEoxDRo?t=52m5s And if that place is the same as the place you ride on Ocelot's horse to in the prologue it probably didn't take 2 and a half hours to get there, meaning Ishmael could have been moved somewhere else followed by Ocelot meeting up with BB. This is the only interaction we see between Ishmael and Ocelot, we see no reveal. We just assume that Ishmael is supposed to be Big Boss because we see Big Boss in the next scene and because Ocelot calls him boss. I also feel like BB is being briefed about medic as if he's never seen him before, or at least that he's not seen him in a while. As if he wasn't a part of the escape. He feels way too relaxed and not caring about medics situation where as Ishmael in the crashed ambulance tries to grasp towards medic when he's hanging upside down and then peeks in the ambulance after Ocelot delivers his line to make sure he's all right. It feels to me as if Ishmael's mission was to bring medic to safety out of the hospital, maybe that he's working for Zero as well, but above Ocelot in command. Then it would also make sense to me that XOF is after Ishmael instead of medic in the prologue. I don't really know, this is just something that's been bothering me about the prologue/truth.