Did Smith kill every person in the Matrix?

Question

We (and Neo) are informed by Morpheus that if you die in the Matrix, you die in the real world:

The body cannot live without the mind.

When Smith absorbed/overwrote every living thing on Earth in his quest for power, he in effect killed everyone in the Matrix. Shouldn't everyone who was plugged into the Matrix have then died in the real world?

Cypher proved this concept to be true when he killed his shipmates in the real world by simply unplugging them from the Matrix (separating their consciousness from their body).

Is this a plot flaw or am I missing something?

Answer 1

No, he didn't kill everyone in the Matrix.

First of all, when Smith takes over an individual in the Matrix, this is probably more akin to when agents temporarily inhabit people. We have seen instances where agents inhabit a Matrix avatar and then leave it, and the character returns to "normal" afterwards (although the helicopter pilot is dead for other reasons — namely Trinity's bullet):

For stronger evidence, there is a scene that I recall in The Animatrix ("Detective Story") where Trinity is followed onto a train by a private eye who has been inhabited by an agent. She shoots the detective in the arm and escapes. Immediately afterwards, the agent leaves the detective and the detective is seen to be completely normal again.

As for programs inhabited / co-opted by Smith, recall that the Oracle is "normal" at the end of Revolutions — further evidence for his actions being temporary rather than "overwriting" anything:

Note in this conversation that the Architect promises to the Oracle that humans in the Matrix who want out "will be freed" — confirming that they are still alive.

Answer 2

No

Smith assimilated every human in the Matrix, but that does not result in death for the assimilated human.

Smith's ability to assimilate people in the Matrix is derived from an Agent's ability to do so, except that Agents are limited to assimilating one individual at a time, whereas Smith can copy himself and in doing so assimilate multiple individuals simultaneously. Agents' assimilation ability restores the possessed individual if the Agent leaves that individual. Usually an Agent leaves the possessed body because the body has sustained a fatal injury (in which case the possessed individual obviously dies), but in some cases we see that the Agent leaves an uninjured body and the possessed individual is restored unharmed (albeit with some memory loss). For example, the comic "Wrong Number" demonstrates this:

It stands to reason that humans assimilated by Smith are similarly restored unharmed except for memory loss.

Furthermore, we see several programs which were assimilated by Smith but which were restored to their original form after he was defeated (e.g. the Oracle and Sati). Most conclusively, the fact that the humans in the Matrix are alive after Smith's defeat is made explicit in the final conversation between the Oracle and the Architect:

The Architect: Just how long do you think this peace is going to last?

The Oracle: As long as it can. What about the others?

The Architect: What others?

The Oracle: The ones that want out.

The Architect: Obviously they will be freed.

The Oracle: I have your word?

The Architect: What do you think I am? Human?

_{transcript for The Matrix Revolutions}

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Note: the original version of the question asked if Smith killed everyone on Earth, not just in the Matrix. I've included the remainder of my original answer to that version for completeness.

Smith did not kill everyone on Earth. There were many humans still alive in Zion after Smith was defeated. In fact, it was because Smith was defeated that the Sentinel army was called off and ended its attack on Zion: Neo made a deal with Deus Ex Machina in which the Machines would end their attack on Zion if Neo defeated Smith:

Neo: The program Smith has grown beyond your control. Soon he will spread through this city, as he spread through the Matrix. You cannot stop him. But I can.

Deus Ex Machina: We don't need you! We need nothing!

Neo: If that's true, then I've made a mistake, and you should kill me now.

Deus Ex Machina: What do you want?

Neo: Peace.

_{transcript for The Matrix Revolutions}

The humans in Zion weren't plugged into the Matrix and hence were safe from Smith.

Answer 3

Given the conversation between the Oracle and Architect discuss human inhabitants of the Matrix who are alive, I'd say there's a bit of a contradiction regarding Smith's assimilation process.

Two things to remember:

1) Neo said it felt "like he was back in that hallway, it felt like death" when describing Smith's attempt to assimilate his just before the burly brawl scene. This implies that the process of assimilation kills the host body.

2) When Smith assimilated Bane, Bane's personality was replaced with Smith's, effectively wiping the human hosts mind. The impression I get from regular agents is they merely take control of avatars, not the actual host.

Extra: the only bodies we see restored are programs - even Neo's body apparently vanished after Smith's deletion.

So, if Smith really did assimilate everyone in the Matrix then to be logically consistent with previously established rules then they should be dead, but apparently aren't. One way to reconcile this is that perhaps Smith didn't actually get everyone in the Matrix since it's never expressly stated as the case. If so this would also explain the implication in the Oracle's exchange with the Architect about people now being aware of what the Matrix is - those that want out will be freed.

Answer 4

Unfortunately I think they died, not because of they were taken over by Agent Smith but because of their consciousness exploded when the Machine AI erased the AS copies, there were no consciousness left in the bodies. So they may have lost every human being, except the new "crop"/babies. It could even be a hole script because the Machines also lost much power when all the people in the Matrix died.