After Neo destroys Smith in M1, Agent Smith becomes obsolete. He's already an exile in M2 and M3. But all agents in the Analyst's Matrix 8.0 became obsolete and were purged, because the Analyst squashes all significant anomalies in the Matrix himself or with bots. He doesn't need agents to do that.
As I point out in Smith: Smith's Survival, the Analyst was forced to deliberately preserve Smith in the Matrix in order to act as Neo's opposite. Remember what the Oracle said about who Smith is:
Neo: What is he [Smith]? Oracle: He is you. Your opposite, your negative, the result of the equation trying to balance itself out. |
Since there were no anomalies anywhere to address in the Analyst's Matrix, Smith's old code and purpose were meaningless. In a bit of approach-avoidance irony, Smith hates anomaly, but without it, he is without any purpose at all. So, in addition to giving Smith an alternate DSI, the Analyst altered Smith's code, giving him the purpose of serving as Neo's corporate boss. The Analyst effectively turned Smith into a kind of bot, or so he thought.
At least a small piece of the old Smith had to be conscious during his imprisonment in the Analyst's Matrix. Otherwise, his anomaly-detecting code wouldn't have been able to set off alarms in his head when he saw Morpheus shooting a machine gun in the Deus Machina building, triggering Smith's old code of countering anomaly in the Matrix. If any other part of the old Smith was "awake" when he was acting as Neo's boss, Smith would have realized that all he could do is wait for an opportunity to take down the Analyst so that the Matrix can return back to the Oracle-based choice model. But such thoughts would have been nearly hopeless, as Smith had no control over himself until anomaly presented itself. It was all up to Neo. Fortunately for Smith, Neo, Bugs and Morpheus came through.
Once Smith emerged in the scene with Morpheus, Smith would have fully seen Morpheus in Matrix code, and Morpheus had to be the most unique anomaly Smith would have ever seen: Morpheus isn't quite a redpill hacker (he's a program), and he's also not quite an exile (he wasn't coded by the Architect). He's a Modal AI who escaped his own Matrix within a Matrix. Maybe Morpheus's code wasn't green or gold... maybe it was purple or pink, to match his flashy personality?
Neo doesn't do anything to create the pandemonium of that scene - the initial waking of Smith is all Morpheus' doing. In fact, Neo is still the Analyst's good little boy in that scene, refusing to fight, telling himself it can't be real. While Smith was able to fully awaken at the slightest hint of seeing Neo or anyone else express anomaly, Smith's freedom here was very short-lived. Immediately after Smith shot Neo in the head, the Analyst reset everything and again squashed anomaly, which would have forced Smith's corporate boss coding to take over again. Smith (the agent/virus) cannot act at all in the absence of anomaly. We don't directly see virus Smith going back to corporate boss Smith, but the yellow words below confirm that it was Neo's exit from the Matrix that freed Smith, not Morpheus' act of redpill terrorism:
Smith: "Once he [Neo] got out, let's just say, I was free to be me."
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This is the nature of Smith's imprisonment in the Analyst's Matrix. He is figuratively chained to Neo:
Smith: You never appreciated our relationship. Not like The Analyst. Morpheus: The what? Neo: My doctor. Smith: He used our bond and turned it into a chain. It’s so obvious once you see it, right? But this whole altered-code update really blew my mind. I still don’t know how he did it. You, as a balding nerd. Hilarious. And me... even more perfect. Maybe a little too far on the piercing blue eyes. What do you think? |
Remember that unlike redpill hackers like Bugs, Smith has never had the privilege of seeing what life is like outside the Matrix. Or, at least, the last time he did was over 60 years ago in the body of Bane-Smith. Therefore, humans have more understanding of the DSI altering process than Smith does:
Bugs: We’ve been tracking that company for years. We screened every Thomas Anderson we found. What we didn’t understand was that they could alter your DSI. Pods generate your digital self-image through a feedback system called Semblance. This is how you look to yourself. Somehow they were able to alter your DSI loop. This is how everyone else sees you.
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Smith would have no way of knowing what the hardware of human pods actually do since Smith is nothing more than software hacking other software in the Matrix.
It's likely that DSIs themselves are subject to the whole "Smith is Neo's opposite" phenomenon. Neo's DSI was altered to be that of a short, fat, loser-looking coder. If Smith's DSI must be the "opposite" of Neo's, maybe that explains why Smith is a sexy, blue-eyed hunk. In that case, the Analyst's altering of Smith's DSI wouldn't be a phenomenon of its own, but instead merely a direct result of altering Neo's DSI.
If DSIs are not subject to this phenomenon of opposites, then altering Smith's DSI shouldn't have been difficult. Smith is just software. In that case, we could read Smith's lines like this, where the green statement is tied to the white statement, but the yellow statement is not:
Smith: But this whole altered-code update really blew my mind. I still don’t know how he did it. You, as a balding nerd. Hilarious. And me... even more perfect.
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The other possibility: this is a plot hole. Lana Wachowski is treating Smith as if he were a human with his own pod and DSI, when really Smith is just a program. A program's DSI shouldn't be difficult to change. In fact, is the appearance of a program even called a DSI? Not that I know of. I think it's just a "shell" as we learned in M3, when Rama-Kandra traded the Oracle's shell deletion codes for Sati's passage through the Trainman into the Matrix. If Smith really is dumbfounded by the "miracle" of altering Smith's DSI, then I can only wonder if Smith himself is a human in a pod (or perhaps he is Bane-Smith resurrected and plugged into the Matrix), which is starting to feel like a conspiratorial and messy rabbit hole.
Let's first start with why Smith killed Neo, a second time. Very simply, Smith couldn't deny his purpose of killing the ultimate anomaly, even if he knows it won't be successful. So as soon as Smith's dormant self emerges, he immediately kills Neo. Unsurprisingly, the Analyst has kill protection in place for Neo (and presumably Trinity), just like we saw in M1 when Neo was killed and then brought back to life.
Then we have the following exchange:
Smith: I have such dreams, Tom. Big dreams. Well, mostly just extremely violent revenge fantasies, but in order for me to pursue mine, I need to dissuade you from pursuing yours. Neo: Hmm. Sounds like conflict. Smith: Inevitable? Doesn’t have to be. All you have to do is stay out of the Matrix, and leave the good doctor to me. Neo: You can have him. I’m here for Trinity. Smith: That’s the trouble, Tom. He knew you’d come, just like I did. Trust me. You’re not ready for him. |
Why would Smith care if Neo goes after Trinity? It's because Smith knows that the Analyst's Matrix is already in the process of quickly toppling down. All he needs is for Neo to stay away, even just for a few days. As far as Smith knows, Neo's attempt to get Trinity out is hopelessly naive and reckless. Smith knows the Analyst has absolute, complete control over the entire Matrix simulation, including Neo and Trinity. If Neo tries to rescue Trinity, Smith knows there is very little chance of success and enormous risk of being captured or using Trinity to leverage Neo's return. Smith has no way of knowing that Rama-Kandra and Kamala gave Sati design plans of the Anomaleum, let alone that there is a plausible plan to rescue Trinity, which (I think) is facilitated by a past or present Oracle (or by Sati having the Oracle's eyes - see Sati). Smith's position here is entirely logical, although for a very different reason than what we'd like: Smith needs to take down the Analyst so the old Matrix model (a model of choice) can allow him to continue trying to destroy everything.
It's easy to miss, but notice the yellow phrase:
Seq: Captain, I’m reading portals from the lower frequencies. Smith: I won’t have his leash on my neck again. I found some old acquaintances of yours. Seq: Bugs! Lexy: Exiles. Berg: I thought they were all purged. Merovingian: You? Oh! It is you! All these years. I can’t believe it. Neo: Oh, God. Merovingian: You stole my life! [speaks in French] Smith: What the Merv is trying to say, is that their situation is a little bit like mine. To have their lives back, yours has to end. |
I think this provides a clue about what Smith did immediately after Neo escaped the Matrix. I believe Smith actively sought out the Merovingian because Smith knew that their goals at this point were temporarily aligned: take down the Analyst by keeping Neo out of the Matrix or by killing Neo. Smith would have been able to take refuge with the Merovingian's Trainman in exchange for the promise to bring the Merovingian and his gang to Neo.
| Bach to Smith |
 Smith: Smith's Survival |
 Oracle |