Title Card: ...5 billion people will die from a deadly virus in 1997... /... The survivors will abandon the surface of he planet... /... Once again the animals will rule the world... / - Excerpts from interview with clinically diagnosed paranoid schizophrenic, April 12, 1990 - Baltimore County Hospital.
The time is the indeterminate future. A virus, deliberately released in 1996 in multiple locations around the world, has killed off five billion people. Survivors have established an elaborate underground civilization because the earth's surface is considered uninhabitable by humans.
From time to time prisoners "volunteer" to don protective gear and gather specimens of insects from the surface to test for the presence of the virus. One such prisoner is James Cole, who after retrieving samples is given the chance to go back in time to 1996 and find information about the group believed responsible, known as "The Army of 12 Monkeys."
Throughout the ensuing episodes, Cole finds himself remembering, as if in dreams, various things that he witnessed as a child, including the killing of a man in an airport. This persists as a theme throughout the film. Miscalculation sends Cole to 1990, and he finds himself incarcerated in an insane asylum.
His psychiatrist, Kathryn Railly, thinks she has met him before, but his ravings are incoherent (to her), and eventually he is locked up with other lunatics. There he meets Jeffrey Goines, who is definitely off the wall, but who tries to help him escape.
Jeffrey: There's the television. It's all right there - all right there. Look, listen, kneel, pray. Commercials! We're not productive anymore. We don't make things anymore. It's all automated. What are we for then? We're consumers, Jim. Yeah. Okay, okay. Buy a lot of stuff, you're a good citizen.
But if you don't buy a lot of stuff, if you don't, what are you then, I ask you? What? Mentally ill. Fact, Jim, fact - if you don't buy things - toilet paper, new cars, computerized yo-yos, electrically-operated sexual devices, stereo systems with brain-implanted headphones, screwdrivers with miniature built-in radar devices, voice-activated computers.
All the doors are locked too. They're protecting the people on the outside from us from the people on the outside who are as crazy as us.
James finds a spider and knows he's got to take it with him, let's it crawl over his hand while deciding what to do with it.
You know what crazy is? Crazy is majority rules. Take germs, for example.
Jeffrey Goines: Uh-huh. In the eighteenth century, no such thing, nada, nothing. No one ever imagined such a thing. No sane person, anyway. Ah! Ah! Along comes this doctor, uh, uh, uh, Semmelweis, Semmelweis. Semmelweis comes along. He's trying to convince people, well, other doctors mainly, that's there's these teeny tiny invisible bad things called germs that get into your body and make you sick.
Ah? He's trying to get doctors to wash their hands. What is this guy? Crazy? Teeny, tiny, invisible? What do you call it? Uh-uh, germs? Huh? What? Now, cut to the 20th century. Last week, as a matter of fact, before I got dragged into this hellhole. I go in to order a burger in this fast food joint, and the guy drops it on the floor.
Jim, he picks it up, he wipes it off, he hands it to me like it's all OK. "What about the germs?" I say. He says, "I don't believe in germs. Germs is just a plot they made up so they can sell you disinfectants and soaps." Now he's crazy, right? See?
James Cole finally takes the spider into his mouth, Jeffrey is either too deep into his talk or unimpressed by this and continues his talk as if nothing happened.
Jeffrey: Ah! Ah! There's no right, there's no wrong, there's only popular opinion. You... you... you believe in germs, right?
Eventually, Cole is snatched back to his present time, interrogated, and given a second chance to complete his mission.
A second miscalculation sends him to the battlefields of World War I, where he is wounded in the leg. However much the result of miscalculation these visits are, they prove instrumental. When the scientists of Cole's present finally succeed in sending him to 1996, Cole kidnaps Dr. Railly and tries to convince her that he is from the future.
He finds that Jeffrey Goines, whose father is a famous virologist, is now out of the asylum, working for his father, and has formed "The Army of 12 Monkeys." Cole is now racing against time, and after a few mishaps, finally decides that he wants to stay in 1996 with Dr. Railly, surrendering to the inevitable destruction of human life.
By this time, Dr. Railly has become convinced that somehow, Cole knows something--his predictions of the outcome of minor events is too uncanny. The discovery of a World War I bullet in Cole's leg forces her to check a photograph taken on the battlefield which, impossibly, shows Cole in the trenches.
She becomes convinced that "The Army of 12 Monkeys" indeed poses a threat, and she persuades Cole to take up his cause again. An essential element in the communication between Cole's past and present is a telephone number where he can leave a message for the scientists of his own present.
When Goines and his "Army" release all the animals in the zoo to roam the streets of New York, and then posts flyers declaring "We did it!" Cole realizes that the "Army" is not the threat, and he leaves a phone message to that effect. Shortly after, Jose, a fellow "volunteer" from the present, approaches Cole with orders for him to complete his mission and hands him a revolver.
Cole initially refuses, but then notices a guard from the present glaring at him. Jose makes it clear Dr Railly will be killed if Cole does not comply. Meanwhile, the police are after Cole for kidnapping Dr. Railly. In an airport, while attempting with Cole to elude capture, Dr. Railly recognizes Dr Peters, a man who worked with Jeffrey Goines's father in the virology lab and "an apocalypse nut".
She rushes to inform Cole of this and frantically identifies him, along with his travel plans, with Jose overhearing this. The man goes through airport screening and manages to persuade security that his biological samples--one for each of the many cities on his itinerary--are harmless. Dr. Railly alerts Cole, and they attempt to stop the man.
To Dr. Railly's horror, Cole is shot by the police while chasing the real perpetrator, who escapes to board his plane. Cole's death is witnessed by a boy named James, who is with his parents: the young Cole. On the plane, the escaped perp takes his seat and gets into conversation with his fellow passenger.
We recognize her as the woman lead scientist from Cole's present. Cole had stated once the virus was located, a scientist would be sent back to study it in its original unmutated form, so that a cure could be developed in the present. She identifies herself as "Jones" and cryptically says she's "in insurance."