If you have not watched 12 Monkeys in its entirety, this page contains what one might call spoilers.
James Cole (Bruce Willis): the protagonist of the film (though some might argue otherwise). He is an underground prisoner in the year 2035, sent back to the year 1996 to trace the development of a deadly virus. The purpose of his travel was to locate the virus in its "original, unmutated state". The scientists of the future/present (2035) would then travel back in time to study the virus and find an antidote for the future. James' original ideas led him to believe that the cause of this virus which would wipe out 99% of humanity in late 1996 was a group known as the 12 Monkeys. He later learns that the 12 Monkeys are actually a group of animal rights activists who plan to release a zoo full of animals onto the streets of New York City. The true spreader of the virus is yet to be discovered ...
Jeffrey Goines (Brad Pitt): activist and fellow mental patient to James Cole. Jeffrey is first seen in 1990 when James Cole is sent to the wrong year in the time continuum. Jeffrey is a patient at a mental hospital and becomes a "friend" of Cole's. It is Jeffrey who helps Cole escape, and it is also Jeffrey who is later revealed as the leader of the 12 Monkeys. Goines is somewhat of a mental case, fidgeting frequently with his fingers and speaking in short, loud bursts. Son of the prominent viroligist, Goines keeps his father's hands full.
Dr. Kathryn Railly (Madelleine Stowe): Doctor of the study of insanity and resident pyschiatrist; Cole's sole love. As far as the timeline of events indicates, she sees a picture of Cole in the background of a WWI photo she had of a man who was diagnosted as insane (this man was Cole's prison friend, Jose). She then meets Cole in 1990 as the resident pyschiatrist of the insane asylum. Cole was found naked, confused and in a violent battle with some city cops. He was arrested, and thrown in jail. She came in and saw him, taking him to the asylum. After Cole's amazing escape, and six years later, Dr. Railly meets Cole outside one of her lectures, and he kidnaps her. Railly and Cole develop an unusual relationship. At one point in the film, she begins to think of herself as insane and realizes that Cole is really a man from the future. At the same time, Cole begins to think he himself is really just insane as she had originally told him, and not a time-traveller. To quote Jeffrey: "You can't turn back time, thank you Einstein. You can't make it be yesterday". The final climax of the movie shows that Railly wasn't just a friend; she was also a savior.