I think Mantis is an ally of Skull Face why? because the soldiers from the hospital are the same XOF soldiers from GZ and since we saw Big Boss later with SF teaming up maybe he becomes a buddy later?
Remember that Psycho Mantis was a part of Big Boss' army, as said at the beginning of MGS1. Something along the lines of FoxHound being comprised of former Outer Heaven soldiers. We can assume Mantis and, perhaps, some genome soldiers were being referred to? I need to watch that scene again.
We don't know much about Psycho Mantis as a kid. According to his bio: when he is an adult he starts his "career" at the KGB, later joins the FBI but goes crazy during a case in 2000 where he delves too deeply into a serial killers mind. He then leaves the FBI and becomes a freelancer untill he joins FOXHOUND, just before the Shadow Moses incident.
More info:
http://metalgear.wikia.com/wiki/Psycho_Mantis
Here is my theory:
I think Psycho Mantis works for Zero and Skull Face. Like I said earlier. I think Skull Face works for Zero but acts like he is opposing Zero.
Like I said earlier. I think Skull Face is acting like he wants to go after Zero. Like in the book 1984: O'Brien (Skull Face) wins over the trust of Winston (Big Boss) and tells him that they have the same goals and that he is part of The Brotherhood (XOF), an organization that wants to take down The Party (The Patriots) and Big Brother (Zero). He then tells him that they all read this book which explains why things are the way they are. He gives this book to Winston, the moment he finishes the book his home gets invaded by the police and he gets thrown into jail and tortured. So you learn that O'Brien wasn't a rebel after all. The Brotherhood was just a way to lure out enemies or people who oppose The Party.
I think there will be more similarities between the book '1984' and TPP. The biggest part of that book is about totalitarianism: total control, rewriting history, doctrinating people and propaganda. I think Zero wants to trick Big Boss and corrupt him. Zero doesn't want Big Boss dead, he needs him. If Zero wanted BB dead he could have bombed that entire hospital and annihilated him. Zero helped create Big Boss' legend status and image and he just wants to have power over him. Like totalitarian leaders want to rewrite books/history Zero wants to rewrite Big Boss.
In '1984' right after O'Brien screws Winston over, and he is sent to jail and tortured he is also being brain washed by The Ministry of Truth. I think part of the reason Big Boss descends into madness is because of Zero corrupting and breaking his mind. Psycho Mantis is there in the hospital is to haunt Big Boss and lets him relive very traumatic experiences. In '1984' O'Brien is torturing/terrorizes Winston with his biggest fear: his fear of rats. He terrorizes him and tries to shape him how he wants Winston to be.
There is another character in '1984' named Emmanuel Goldstein which could also relate to Big Boss. Goldstein is one of the founding members of The Party (The Patriots) just like BB, he also breaks away and starts his own organization. He is then regarded as an enemy of the state by The Party.
TL;DR Read the book '1984'. :>