Jupiter Jones was born under a night sky, with signs predicting that she was destined for great things. Now grown, Jupiter dreams of the stars but wakes up to the cold reality of a job cleaning toilets and an endless run of bad breaks. Only when Caine, a genetically engineered ex-military hunter, arrives on Earth to track her down does Jupiter begin to glimpse the fate that has been waiting for her all along.

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.

In an anti-utopian future, the "real" world as we know it is nothing more than a computer construct, created by an all-powerful artificial intelligence. A small group of humans as found a way out of the construct, and are now fighting for the future of the human race.