Although the director Gilliam has himself said that he wanted the film to be ambivalent and to be about perception of the reality, I would like to amplify on his statement.
I see this flim as an exploration of the psyche of a really sensitive little boy who was traumatized and somewhere along had to be put in a mental asylum.
James Cole, a little boy witnesses a violent shoot out, death and immediate emotional consequence of death out of the blue, this event scars him for life and negatively affects his sensitive psyche.
A sensational 24X7 media coverage of a little boy falling deep underground into a horrible situation with which this boy supposedly struggles for days to come, the outcome of this episode is that it was all a "hoax", that it was a prank, the boy was hiding in the barn, nothing serious, it could be a hint or reflection of the actuality of all the apocalyptic "reality" james claims that it is a "hoax" a mere imagination.
Most probably James became paranoid schizophrenic and was put in a mental asylum where he might have dissociated from reality and got lost in a wonderland where he was a "prisoner" and that this mental asylum is actually an "underground" totally "disconnected from the outer world" base of humans who are survivors of some sort of viral plague which has devastated humanity, which in itself again is a paranoidal dystopian view, no wonder that after early childhood traumas James might have developed morbid and gloomy worldview where he must be believing that "humans are endangered species" , "everybody will die", "world will doom".
There are a lot of evidence / similariteis that the mental asylum is infact the underground human set-up such as -
- The similar and strikingly resembling panel of examiners/doctors/scientists in both worlds
- Similar facility of holding patients / prisoners
- James in restraints at both places
- Absence of young, desirable women in both places
- Both places are completely disconnected from "outside" world
and much more
We see that Dr. Railley is somewhat compassionate with James to the point that she convinces the panel of doctors to let James make the call to the future humans, this is a hint that the doctors and Railley both can go along and participate in the imaginary events of James, that is why it is possible that Railley in later part of the movie agrees to James and sort of becomes his companion, also we need to understand the fact that we never see faces of James's parents which is a message from the film that James wasnt very close to his parents or that his parents werent there for him when he needed them emotionally, which means that Dr. Railley could be simply playing along as part of therapy as she knows that love and support can sometimes cure such patients.
We see many hints that whatever vision (reality for James) James has for the future post-apocalyptic world - a lion, apex predator, on apex of the building, a bear etc. were fueled or triggered by visionary or audible cues like the picture of the bear in the snow on a storefront back in 1996, sound of a lions roar playing in the headquarters of animal rights people etc. when infact the animals freed from the zoo were freed in 96 and couldnt survive for another 40 years so how is it that James encountered those animals when he is sent to probe on the surface in 2035.
I see this film connecting with many other flims like Fight Club, They Live, Sucker Punch, Gaslighting, Wizards of Oz etc. In Fight Club which is again about a person who dissociates with reality and becomes "mentally divergent" and thinks of himself as some apocalypse advocate, where again Brad Pitt heads a cult like group and trains space "monkeys", in one scene Brad Pitt says in 12 monkeys that he will "shave your head" exactly what he does to the members of fight club.
It is possible that everytime James Cole is sent back to the "past" that he is actually being sent into outer, open world for observation that if he could blend in and survive in the out and can lead a normal life and I think Railley could be the one suggesting this step and thus helping him out on this.
One more point which compells me to believe that James is imagining things is that there are not much details about the underground world or lives of humans and about how did James end up as a prisoner,it is just a dystopian and underground version of a prison or mental asylum of the normal world, a reflection of it.
I also remember someone saying in the film that "you can not prove anything", I dont remember exact line, but something in the lines of this theory or argument called Boltzmann Brain where it deductively says that only the existence of your Brain can be proved and existence of nothing else can be proved in the whole universe as it can be all just an imagination of your brain as there is a higher probability of such a brain existing when compared to the probability of eexistence of such meticulous huge universe in actuality.
All this and much more I can not remember from top of my mind suggests that 12 monkeys is about perception of reality explored through a character who is unfortunately become a classic subject for this particular study in the story.