I think my “trinity”, he refers to the Christian doctrine where God is a single being but exists in three forms: father, son, and spirit. So how Mr. Smith can be both program and human can sort of explain how Jesus is both God and man, etc.
I’d take a fair shot at the matter, but thinking through all the vague and contradictory statements from the second and third movie is giving me a major headache. Long story short, my theory is that agent Smith is merely implanting his program into the machine implants on the human body and takes control of all the motor action, mind control style. Since the host body’s mind is intact (and merely overtaken), the Smith program is merely a program interacting through a human interface, not merged with the human mind.
Extensive thought process rambling of an insane mad man follows:
To figure out how the who “Smith in a human body” deal works, we need to figure out how agent Smith is cloning himself in the first place…
My take on it is that his ability to clone is merely an unrestricted version of the original Matrix agent program. There are plenty of example of agent programs at work - the agents would switch body with one of the minds hooked into the Matrix. The curious thing is, while a mind that is under agent control is basically written over with the agent program, it nevertheless suffers the consequences that the agent suffers - for example, when Trinity kills an agent in the first movie, the agent program releases itself from the host and the host mind dies - but the agent program itself doesn’t, and quickly installs itself into a new host.
My conclusion is that the agent program requires a human mind “interface” to operate, but the human mind continues to exist at this point - it explains why destroying Smith at the very end allows all the cloned bodies to return to normal - the program is destroyed at the source by having Neo enter the Smith program directly, not through the interface i.e. destroying a mind through the matrix.
So agent Smith’s ability to clone himself over multiple bodies is basically just having old restrictions lifted from his program (being “free”) because he got an imprint of the Neo program. I’m guessing this also lifts the restriction of staying in the Matrix (instead of jacking out with a human)… the normal agents can’t do it because policing the Matrix is their program parameters. By and large when an agent overrides a mind they can make use of every function of a human brain - they just don’t know how to deal with physical motor controls because it’s not part of the program and they’re not suppose to jack out anyway, so it’s all moot to them.
Speaking from a practical standpoint, in order for agent Smith to jack out with another human being he’ll need some sort of storage for his own program - since, if you remember, the mind still exists but merely hibernates while the program takes over. And instead of doing the curious but excessive thing of imprinting himself over a part of the physical brain, he merely need to take over some piece of self-sustaining machine implants that’s born with every human battery. From that point he can manipulate the brain into doing whatever he wants - although curiously it is highly likely that this “copy” of Smith is acting independent of the original Smith collective since its direct connection to the Matrix had been severed (although if you really want to stretch it, I’m sure somebody down at Zion has a wireless router to the Matrix… right? right?). Anyway, because in this scenario the machine and the human components are separate I’d have to say Bane is still human and Smith is still a program, no crossovers here. I mean, just grafting a toaster machine onto one of my arms doesn’t make me fully toaster and fully human, right?