AIt does, according to director Terry Gilliam. Cole's mission was never to change the past, which he repeatedly states cannot be done, but rather to find a sample of the pure virus which could be sent back to his time for analysis, in hopes that they could at least create a cure for al the virus' mutations, and make the Earth habitable again in that future. At the end of the film, Cole identifies the carrier of the virus, and although Cole himself dies, his information allowed one of the scientists to go to the past from the future, and obtain a sample of the virus, thereby making the hope for an eventual cure possible. Note that the female scientist is clearly the same age in the modern setting as she is in the future scenes, ruling out the notion that her younger self just happens to have been on the plane with the carrier. It is strongly implied that the scientists from the future planned Cole's death because he refused to return to his own time, and they could not allow him to disturb the past any further. They send Jose (Jon Seda) through time to give Cole an ancient gun and instructions to complete his mission. They might have intended that Cole try to use the gun in a(n) (futile) attempt to kill the carrier of the virus. The scientists probably knew it would not work and would cause security personnel to neutralize him, while the female scientist herself made sure the mission was completed.
AIt's called 'The Earth Died Screaming' by Tom Waits. The complete 12 Monkeys soundtrack can be found here with scene descriptions. Waits had a cameo appearance as a homeless veteran in Gilliam's previous film, The Fisher King.
AThe Army of the Twelve Monkeys is inspired by a passage in L. Frank Baum's novel, "The Magic of Oz," in which the Nome King and Kiki Aru convince twelve monkeys that they will have an endless supply of food if they become human soldiers for them.
