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.

Mysterious deaths and unexplained disappearances begin to occur in the small seaport village of Graves Point. When a large, strange claw is discovered on an empty raft washing up on the shore, marine biologist Dr. Herbert Talley identifies it as belonging to a rare giant squid.

After an accident during a routine trip to Venus, a spaceship has only enough oxygen left for three people... out of five on board.