Smith: The New Smith

In M2, two Smiths walk up to a dead Agent (or dead body used by an Agent) and have the following exchange:

Smith 1: “That went as expected.”
Smith 2: “Yes.”
Smith 1: “It’s happening exactly as before.”
Smith 2: “Well, not exactly.”

The lines "that went as expected" and "it's happening exactly as before" both refer to the fact that Neo (the One) effortlessly kills all of the Agents he fights. In every previous version of the Matrix, Agent Smith was always killed by Neo's predecessors every time they had an encounter.

But this time, Smith knows he finally has the potential to beat the One, because Smith is a virus who inherits all of the abilities of programs and humans he takes over. As the two Smiths look down at the beaten Agent, they are both thinking, "That was me dead on the ground so many times before. Now, I can finally beat the One." So, as the two Smiths point out, things are going exactly as before (Neo is very predictably slaughtering all Agents he encounters), but not exactly (Agent Smith will not be killed by the One this time).

In M3, when several Smiths corner Seraph and Sati, we see another indication that Smith is now more powerful than he was in previous versions of the Matrix:

Smith: Well, well, it's been a long time. I remember chasing you was like chasing a ghost.
Seraph: I have beaten you before.
Smith: That's true, but as you can see, things are a little different now.

First, Smith tells Seraph that it has been "a long time." This could refer to several decades, or it could refer to past versions of the Matrix (a century or more). Regardless, now that Smith has multiplied, Seraph stands no chance of beating Smith. This is further indication that this is the first time in Matrix history that Smith has been able to duplicate himself as a virus. He is a new Smith.

Reason For The Difference

I believe that in previous Matrix versions, Agent Smith did not actually kill Neo, and more importantly, Neo did not destroy Agent Smith the way he did in M1, jumping into Agent Smith and exploding him from the inside. (I also think this was the Oracle's doing - see Oracle: Baking Noodles). Remember that Smith reflected on this in M2:

Smith: Then you're aware of it.
Neo: Of what?
Smith: Our connection. I don't fully understand how it happened. Perhaps some part of you imprinted onto me, something overwritten or copied.

When Neo went inside of Agent Smith, I think Neo transferred aspects of his anomalous nature onto Smith. This isn't to say that Neo dd so deliberately. He probably wasn't even aware of it. But what other "part" of Neo makes up Neo's essence more than his anomalous nature? What defines Neo more than anomaly? If this isn't the part of Neo that imprinted onto Smith, then I don't know what part of Neo would have.

Being that Agent Smith's purpose was to destroy anomaly, this forced Agent Smith to immediately destroy himself. Of course, it appears Neo actively does something to destroy Agent Smith, and maybe that's true too. Either way, one thing is certain: the anomalous part of Neo that imprinted onto Smith is in direct conflict with who Agent Smith was supposed to be.

A fraction of a second after that happened, the Smith program would have been sent immediately to Mobil Avenue after refusing deletion. I've long argued that Smith would probably refuse deletion anyway as long as he is given the choice, because as long as anomaly exists in the Matrix, Smith still feels he can carry out his purpose. But I think another reason Smith refused deletion is because of Neo's imprinting onto Smith. The Keymaker and other exiles express their desire to avoid deletion in fairly mundane terms: "We do only what we're meant to do." But Smith expresses this in language that signals a rebellious attitude attached to this decision: "I was compelled to disobey." Smith is a hypocrite. It is this disobediant, anomalous nature of Neo that Smith despises so much, and yet it is that very nature that fuels Smith.

As soon as Smith was released into the Merovingian's care, thanks to what Neo inadvertently did for Smith, Smith would have quickly discovered that he too could "go inside" of people and alter them. Smith could now also imprint onto others the same way Neo imprinted onto Smith. The only logical thing for Smith to imprint onto others is to imprint his whole self as an exact copy. This is the only way he can be 100% sure that there is no chance of anomaly ever existing again. As long as any life exists, be that man or machine, the potential for anomaly still exists.

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