Renowned paleontologist Dr. Grant is tricked into a plane going over InGen's former breeding ground for prehistoric dinosaurs. When their plane crashes and a small group becomes stranded, they discover the island's native inhabitants are smarter, faster, fiercer and more brutal than imagined.

Neo, Trinity, and Morpheus continue to lead the revolt against the Machine Army. In their quest to save the human race from extinction, they gain greater insight into the construction of The Matrix and Neo's pivotal role in the fate of mankind.