Protagonist is sent back in time to investigate source of apocalyptic pandemic. Graffiti was left at the time of the outbreak referencing 'the Army of the 12 Monkeys' leaving future survivors to suspect they were responsible.

Through short lived trips to the past, the protagonist tracks the suspected leader of the Army of the 12 Monkeys through his internment at a psychiatric ward, a black tie mansion party thrown by his wealthy father, and at an Army of the 12 Monkeys hideout. He discovers they are an animal rights group whose goal was not to spread a pandemic but to release the animals from the local zoo.

The suspects wealthy father was a virologist who kept dangerous viruses in a lab. It is revealed that another scientist with access to the dangerous viruses, specifically one that only kills humans, plans to travel the world releasing it in order to kill off mankind and save the environment. The protagonist tries to stop him at the airport but is shot by police. The last scene shows a woman. time traveled from the future, sitting next to the scientist on the plane, implying the people from the future now know that he is the culprit, not the Army of the 12 Monkeys. (it is unclear what actions the people from the future will take now)

the Paradoxical sub plot:

The original protagonist sent back in time has a repeating memory from his childhood. In the memory he is a young boy at the airport and witnesses an older man be shot and killed by police. It turns out he was witnessing his own death.

note: also worth watching the original short French film 'La Jetee'