In the year 2035, convict James Cole reluctantly volunteers to be sent back in time to discover the origin of a deadly virus that wiped out nearly all of the earth's population and forced the survivors into underground communities. But when Cole is mistakenly sent to 1990 instead of 1996, he's arrested and locked up in a mental hospital. There he meets psychiatrist Dr. Kathryn Railly, and patient Jeffrey Goines, the son of a famous virus expert, who may hold the key to the mysterious rogue group, the Army of the 12 Monkeys, thought to be responsible for unleashing the killer disease.

When an asteroid threatens to collide with Earth, NASA honcho Dan Truman determines the only way to stop it is to drill into its surface and detonate a nuclear bomb. This leads him to renowned driller Harry Stamper, who agrees to helm the dangerous space mission provided he can bring along his own hotshot crew. Among them is the cocksure A.J. who Harry thinks isn't good enough for his daughter, until the mission proves otherwise.

Following an unexpected tragedy, child psychologist Malcolm Crowe meets a nine year old boy named Cole Sear, who is hiding a dark secret.