Science teacher Ryland Grace wakes up on a spaceship light years from home with no recollection of who he is or how he got there. As his memory returns, he begins to uncover his mission: solve the riddle of the mysterious substance causing the sun to die out. He must call on his scientific knowledge and unorthodox ideas to save everything on Earth from extinction.

The human city of Zion defends itself against the massive invasion of the machines as Neo fights to end the war at another front while also opposing the rogue Agent Smith.