Jiminy Cricket, a vagabond insect, spends a rainy night at the shop of toymaker Geppetto. The Blue Fairy brings a marionette to life after Geppetto wishes on a star for a son, and Jiminy Cricket is appointed the new boy's conscience. He has a devil of a time keeping up as Pinocchio is willingly lured through various forms of temptation, the most frightening of which leads him to Pleasure Island, where he drinks, smokes, and is almost turned into a jackass.

Dutch and his group of commandos are hired by the CIA to rescue downed airmen from guerillas in a Central American jungle. The mission goes well but as they return they find that something is hunting them. Nearly invisible, it blends in with the forest, taking trophies from the bodies of it's victims as it goes along. Occasionally seeing through it's eyes, the audience sees it is an intelligent alien hunter, hunting them for sport, killing them off one at a time.

Spanning over one thousand years, and three parallel stories, The Fountain is a story of love, death, spirituality, and the fragility of our existence in this world.