What was the story of 12 monkeys really about?

The film itself is not, and never was, about stopping the spreading of the virus. The scientists in the future know that they cannot stop the spread because it has already happened. What they require is a sample of the original, pure virus that they can then study and create a cure/antibody for thus enabling the human race to return to the surface of the planet.

At the start of the film, they believe the virus is something to do with a group called the 12 Monkeys, but they need proof. This is where Bruce Willis comes into it. Through his efforts, they eventually find the man who spreads the virus at which point one of the scientists is sent back to make contact with the plane which we see in the final scene of the film.

The story of 12 Monkeys is about perception v. reality. And time travel. And several other "deeper" things.

There's a scene in the film, near the finale, where Cole (Bruce Willis) is commenting about a movie he knows he's seen before which seems somehow different to him. He concludes the movie itself is static - it's filmed, it cannot be changed - but it nevertheless does, in fact, seem different because he (the viewer) has changed, which alters his perception and interpretation of the work. Based on what you've taken away from 12 Monkeys, I would suggest you view the film again at some future date and hopefully experience this phenomenon first hand.

The "dream" does not "come true". Bruce's character, Cole, has a memory from his childhood where he sees a man get shot in an airport. This experience is traumatic and gives him an uncommon strength of mind. This experience was totally real, and Cole remembers it.

This strength of mind and his status as a criminal (which I don't remember being explained) make him a candidate for the time travel experiment. Twelve Monkeys style time travel is apparently rough on your mind. We see Cole struggling to remember his instructions (finding a spider and eating it?), and the names of Cities. Not everyone is up to it, but Cole is.

Cole ends up going back in time, one more time, because he's in love, winds up at the airport, and we see those events that he remembers, but this time with Cole as an adult.

It's a mild predestination paradox. Cole can be a time traveler because he saw himself get killed, and he only got killed because he was a time traveler.

The movie was inspired by the French Film La Jetée, discussed in this question, in which a narrator explains most of this briefly.

As for whether the scientist/"insurance" agent lady is there to prevent the plague, get a sample of the disease, or is there by total accident, there is a lot of debate, like here.

A few things.

1. The 'future' is a prison-like meager existence underground dystopia, somehow has the STEM technological wisdom and capability to travel through time, but fails to realize they are the antibody as survivors and lack the wherewithal to produce the cure for a virus using its own subjects as a source for antibodies? No. If Cole can go to the surface and get a spider to eat, then why has he not come back infected? This entire sequence is laden with clues of child-like, flawed imagination, as does Cole's entire performance -- he behaves like a daydreaming child throughout.

2. If time travel somehow is an asset of some future underground dystopia as postulated by the narrative, then the virus source came from Cole or the other time travelers in much the same way European exploration brought disease and plague to the New World. Not likely.

3. We don't know from who's perspective the story is told: a child's imagination as a result of an incident at an airport or from the mind of a mad man....or perhaps the good Doctor Railly in the midst of a bout of a Cassandra complex of her own. Who is telling the story?

It's a psychological thriller which means it's basis predominantly lies in perception.

When the lady says she is in insurance, she means she is there to ensure that the virus does not spread and the planet is saved. Cole did his job of finding out who the real culprit was in spreading the disease, and her job presumably to kill him. My guess is she does just that and humanity is saved, but you just never know.

"So what is going on really? From whose perspective did Bruce see all this happening? From his dream, it seemed like there was a third version of Bruce that saw everything happening".

12 Monkeys studies the subjective nature of memories and their effect on perceptions of reality. Examples of false memories include Cole's recollection of the airport shooting, altered each time he has the dream, and a "mentally divergent" man at the asylum who has false memories.

The short answer is that it's left up to the viewer to interpret the truth of the reality, being either a story about:

1. A boy named James Cole who was traumatized by an incident at an airport to the extent that as an adult living in a mental institution he is making up a Dystopian time travel story about a future where man was nearly wiped out by a virus...
2. or a man named James Cole who lives in a future where, as a felon forced to live underground, he is tasked by scientists with time traveling back to figure out who or what caused the virus in the first place in order to acquire a cure, and in which he has memories or a premonition recurring from childhood of an incident that has yet to happen to his adult self that comes to pass at the end of the film (aka a paradox).

As many answers point out, you can find "flaws" or poke holes in both interpretations to the story that might sway a viewer to pick one interpretation over the other (I however lean towards time travel with some kind of lightly altering casualty loop with not enough evidence to prove dramatic change to what may be the original time line or the previous iteration).

This is why this film would be categorized as a psychological thriller, because it's been designed for the viewer to constantly contest the nature of the characters' reality, as they move through the film and/or viewers may be left with questions and ambiguity still by the film's end in NOT being able to determine the full truth.

In this case the film is also playing with what is known as Cassandra Complex, relating to a metaphor originating from a Greek Mythological figure that believes: some things could be known in advance but not prevented.

The term originates in Greek mythology. Cassandra was a daughter of Priam, the King of Troy. Struck by her beauty, Apollo provided her with the gift of prophecy, but when Cassandra refused Apollo's romantic advances, he placed a curse ensuring that nobody would believe her warnings. Cassandra was left with the knowledge of future events, but could neither alter these events nor convince others of the validity of her predictions.

The metaphor has been applied in a variety of contexts, such as psychology, environmentalism, politics, science, cinema, the corporate world, and philosophy, and has been in circulation since at least 1949, when French philosopher Gaston Bachelard coined the term "Cassandra Complex" to refer to a belief that things could be known in advance.

This relates to the film in both that Cole knew about the "dream" of seeing himself and Cassandra (character also called Cassy) at the airport, but never took it seriously or knew how to apply it to his situation (as it kept "altering" each time he "remembered" it), playing into the tragedy of his character's story and the irony in that the scientists believed that they couldn't change the future by altering the past, by trying to prevent it. It never seems to cross their mind. They're only interested in the past in hopes of finding a cure, when Cole's memory suggest, they might have been able to dramatically change the future.

Just saw this movie and I think the story is being told by the little boy that was in the barn.

The first hint is in the mental ward where the black patient talks about his mind diverging to outer space, escaping his painful reality. I think this ward specialized in those patients. After kidnapping the psychiatrist James talks about crying wolf as a kid with that story, but something happened after, the movie didn't say what, as a kid to James.

I think he was really trapped underground, in a well perhaps, because there are a few references to tunnels in the movie. People probably didn't look for him right away because they remembered the barn incident and so he was in there awhile presumably. James hints of this when he was listening to the story on the car radio. He asks to change the station because he couldn't bear listening.

I think the psychiatrist was his psychiatrist as a child in real life after something happened to him and this is why she feels he looks familiar even in the first scene where they met. Just as the black mental patient, James has delusions of grandeur where he believes he has a strong mind and only he can save the world. I really liked this movie because it appears on the surface that it's about time travel, but it's actually about mental illness.

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 -

1. The similar and strikingly resembling panel of examiners/doctors/scientists in both worlds
2. Similar facility of holding patients / prisoners
3. James in restraints at both places
4. Absence of young, desirable women in both places
5. 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.