There's only a few movies around where the bad guys win and general audiences will tolerate it. The most recent example would probably be "The Dark Knight" and even "The Empire Strikes Back". In most of these interpretations the audience takes solace in the fact that the good guys will get them in the next installment. Rarer still are films like "Twelve Monkeys", where there seems to be no hope of escaping immanent doom. The story revolves around a man sent back in time several times in order to collect information to prevent the release of a deadly virus that kills billions. The end proves to be extremely fatalist, as the actions taken by the future to find a cure cause the creation and spread of the virus in the past.
All things aside the writing seems to be the most appealing part of this film for me. All of the bizarre psychological concepts introduced throughout the story makes you start to question the sanity of just about everyone appearing in the film. It also manages to weave little intricate details all around to be tied up by the end. While the film seems open to interpretation, I felt the overall theme to be nihilistic. It doesn't matter whether the world ends tomorrow or if you're crazy; believe or do whatever makes you happy. There's still a few plotholes that can be chalked up to the fact that there's about a thousand different theories on how time and theoretical time travel works.
Another thing that I thought was done well was the acting. I don't think I've ever seen Brad Pitt play such a convincingly crazy character, and Bruce Willis pulls off the quiet disturbed type very well. When I saw Christopher Plummer's name in the credits I assumed he was going to have a bigger part than he turned out having. I was admitedly disappointed that he only got about five to ten minutes of screen time total.
"Twelve Monkeys" is a movie that will probably make you depressed about the world. It's bleak, future noir at some of it's best. That being said, a lot of the visual eyecandy you'd associate with the genre takes a back seat to the story, which I admire. There's only really a few moments spread throughout the film that have fantastical elements in them. Everything else is produced by Bruce Willis' interaction with the modern world of the 1990s. It will also make you think about a lot of things. My take on sci fi is that if it's good it makes you think, and that's definitely something this movie can do.