I misunderstood the premise the thread, and assumed that you were asking for a song which contained the germ of a whole movie. In which case I would have nominated Bob Dylan's "Rosemary, Lil, and the Jack of Hearts." But never mind
I don't know about one song, but Radiohead's OK Computer totally syncs with 12 Monkeys with Brad Pitt.
Metallica's One and Johnny Got His Gun (happens to be on the phone now!) That's kind of cheating since the band purchased rights to the movie to make the music video but still.