Prediction: Sam Flynn returns to Encom and fires Dillinger Jr. Before he leaves, Dillinger discovers the secrets of the Grid and steals the "disc" while Sam isn't looking. He then creates a new Grid in his own image and from this new Grid, a superior form of AI emerges into the real world. Dillinger Jr. builds a new company based on his discoveries, which he calls Skynet. Unfortunately, his creations become self aware and threaten to take over our world.
Sam and Quorra are the only ones who can stop this from happening. In order to do so, they must convince Dillinger Jr. to give them access to the new Grid. Once inside, they discover that the new Grid is far more dangerous than the old one. Luckily, they discover more beings like Quorra who join them, forming the Resistance.
Meanwhile, back in the real world, the machines have either killed or enslaved the entire human race, but for a handful. In a last ditch effort, the remaining free humans launch a nuclear assault on the machines before retreating deep underground. The machines survive the assault but, in order to survive the nuclear winter that follows, they must find a new source of energy.
By the end of the movie, it becomes clear that this is not a war that will be settled in a matter of days, weeks, months, or even a few years, but that it may take decades. But hope is rekindled. In this chaos, a miracle occurs. Sam and Quorra give birth to a child (part human, part digital being) and a prophesy is foretold that this child will bring freedom to both human kind and the digital world. His name...Neo.
