Zion is a city, far below the scorched surface of the earth, where free humans live. The citizens of Zion are both former inhabitants of the Matrix who have been freed, and also "100% home-grown humans" that have never been slaves to the Matrix.

Many of the extras in this scene are twins, creating a "copy-paste" computer program feel.

Disillusioned with life outside the Matrix, and regretting his decision to become a "redpill", Cypher strikes a bargain with Agent Smith to return him to the Matrix and erase his memory of ever awakening. In exchange, he will betray Morpheus.

Neo sees a black cat repeat its own actions, and mentions "déjà vu". This alerts the others to a possible trap, as they explain that déjà vu is a glitch in the Matrix caused when something is changed.

After humans scorched the sky to cut off solar power, which was the machines' primary source of energy, the machines adapted to use the humans as their power source. Morpheus states: "The human body generates more bioelectricity than a 120-volt battery and over 25,000 BTUs of body heat. Combined with a form of fusion, the machines had found all the energy they would ever need. There are fields, Neo, endless fields where human beings are no longer born. We are grown..."

Switch refers to Neo as "coppertop", another name for the Duracell battery. Later Morpheus holds up a battery as he explains to Neo how the humans are now the energy source for the machines.

Agent Smith explains that the first versions of the Matrix looked like a paradise, but the majority of the people hooked to the Matrix rejected that "reality" as fake. He suggests instead that adversity and suffering are part of human life, so their world needed to reflect that for the human mind to accept it as "real".

In describing humans, Smith says, "There is another organism on this planet that follows the same pattern. Do you know what it is? A virus. Human beings are a disease, a cancer of this planet. You're a plague and we are the cure."

In The Matrix Reloaded, Smith reveals that his encounter with Neo severed his connection with the Matrix and has made him a rogue program.

The Oracle tells Neo that he will need help from the Keymaker in order to reach the Source, the machine mainframe. The Keymaker is a program that creates shortcut commands, physically represented as keys, that can be used to gain quick access to various areas within the Matrix.