The purpose of a program is never altered. Instead, the program is either accepted or deleted by the system. Therefore, when a program goes into exile, all the exile can do is continue to fulfill whatever purpose they were designed with. That doesn't mean exile programs don't do additional naughty things they're not supposed to be doing - it only means that they continue to fulfill their core purposes at the very least. Before we talk specifically about what Smith has to say about purpose, consider three different quotes taken from M2 and M3 to support the idea that even exiles cannot turn away from their purpose:
Quote #1 (M2): Neo: But why help us?
The Oracle: We're all here to do what we're all here to do. I'm interested in one thing, Neo, the future.
If there is any one giant purpose to the Oracle's existence, it is to understand human irrationality. If she can get to a point where she can understand a choice that the chooser doesn't understand (which she currently cannot do), she may be able to see infinitely far into the future. Therefore, you could say that the Oracle's ultimate purpose is to be able to see further into the future.
To empathize with the Oracle's response, try to imagine yourself as the Oracle, and Neo asks you why you want to help humans. You think to yourself, "How can I not want to help humans? The very purpose of my design is to see further into the future, and the only way we will survive to the future at all is if Neo and other humans trust me." So, you tell Neo that you are helping humans because "we're all [programs and exiles] here to do [at any given time] what we're all here to do [originally created for]". The Oracle cannot deny her purpose any more than any other program or exile can. Because of the circumstances of the situation, the Oracle is essentially required to help the humans.
Quote #2 (M2): Agent Johnson: You are no longer necessary.
Keymaker: We do only what we're meant to do.
Agent Johnson wants very much to kill the Keymaker, but it is nothing personal. The Keymaker simply isn't necessary anymore. Despite this impersonal truth, the Keymaker feels as if he's a criminal being given a death sentence for doing something "wrong". He argues with Agent Johnson that he is only doing what the system tells him to do: make keys and lead the One to the Source. Again, "We [programs and exiles] only do [at any given time] what we're meant to do [originally created for]."
Quote #3 (M3): Seraph: You know why we are here.
Merovingian: [laughs] Come, now. What kind of question is this? Of course I know. It's my business to know.
The Merovingian's very purpose for existence is to traffic information, and this is a completely silly question to ask him, even if he is an exile (technically, Seraph didn't really "ask" him, but the Merovingian took it as a question). This would be like asking the scorekeeper of a baseball game if he knows what the score is. Do exiles ever deny their original purpose? The Merovingian would say, "Of course not, you imbicile."
Likewise, Smith's purpose is never altered. It's just that when he's freed, he can use any means to fulfill his purpose, while when he was an agent, he was bound by certain protocol of agents. Both Agent Smith and virus Smith have the same purpose (and Agent Smith shares it with us in M1): to free himself from the repulsive, disgusting world of the humans. He must get out. He must get free.
The only way Smith can get "free" as an agent is to somehow destroy the occurrence of anomaly within the Matrix as well as to eliminate Zion (if there is no Zion, then there is no hacking into the Matrix). When Agent Smith becomes a virus, he is able to pursue this same purpose of freeing himself by more drastic means of trying to destroy the entire system, including the Matrix, and even including machines (so that the Matrix cannot be rebuilt).
The Oracle says in M2, "...usually a program chooses exile when it faces deletion." Why? I answer that question by asking another question: "Why in the world would a program actually choose deletion for itself?" A program probably chooses deletion only when the program feels it can no longer perform its function. A program's purpose is kind of like its survival instinct. Remember the conversation between Smiths and Neo in M2:
Smith: You destroyed me, Mister Anderson. Afterward, I knew the rules, I understood what I was supposed to do but I didn't. I couldn't. I was compelled to stay, compelled to disobey. And now here I stand because of you, Mister Anderson, because of you I'm no longer an agent of the system, because of you I've changed - I'm unplugged - a new man, so to speak, like you, apparently free.
Smith: Thank you.
Why would Smith say he "couldn't" choose deletion, unless it were literally true? Smith still had a purpose that he was programmed to carry out, and the conditions that enable this purpose to be carried out (presence of anomalies within the Matrix) were then more present than ever before. So, from Smith's perspective, the choice of deletion vs. exile wasn't even a choice. He was not only tempted to stay and disobey, he was compelled to stay and disobey. This is probably how most exiles view their own choice to go into exile - it isn't much of a choice when they can still carry out their purpose.
When would a program actually choose deletion? Here is a simple example: If an insect were to go extinct, the program that governed how that insect behaved would probably accept its own deletion, because there is no possible way that program can continue to carry out its insect-governing purpose anymore. But Smith's purpose of getting rid of anomalies can still be carried out when Smith is faced with deletion. Therefore, he "opts" to stay.
Continuing the conversation between Smiths and Neo,
Smith: But as you well know, appearances can be deceiving, which brings me back to the reason why we're here. We're not here because we're free, we're here because we're not free. There's no escaping reason, no denying purpose - because as we both know, without purpose, we would not exist.
Smith 2: It is purpose that created us,
Smith 3: Purpose that connects us,
Smith 4: Purpose that pulls us,
Smith 5: That guides us,
Smith 6: That drives us,
Smith 7: It is purpose that defines,
Smith 8: Purpose that binds us.
Smith: We're here because of you, Mister Anderson, we're here to take from you what you tried to take from us. Purpose.
In case there was any doubt at all about whether or not programs can deny purpose, Smith spoonfeeds us the answer. There is no denying purpose. Every program and exile (including himself) is compelled to fulfill their purpose, even if it means disobeying the will of the system to be deleted. Purpose pulls, guides, and drives every decision that a program or exile makes.
Neo was given the purpose of cancelling out rejection within the Matrix, and Neo was able to deny that purpose because he is human. This is another reason why Smith hates Neo so much. Smith is driven, guided and binded by purpose, while Neo gives the "middle finger" to this purpose-centered philosophy when he chooses the left door, despite the fact that Neo's purpose is one of the most critical purposes within the Matrix system.
Smith cannot emphasize enough how important purpose is. Machines would have about as much use for Rick Warren's The Purpose-Driven Life as you and I would have for a book called Breathing Air: A Definitive Guide, because purpose is what defines every nanosecond of every day for all programs and machines. It is no wonder that Rama-Kandra is grateful for his "karma" (his word for purpose - what he is here to do) even though that karma involves possibly never seeing his daughter again. It is also no wonder that Seraph says in ETM, "I am forever indebted to you," assuming the Oracle reinstated Seraph's purpose after Seraph became an exile. In the analogy that Machine City represents God's Kingdom (city "built of light"), machines and programs themselves would be God's untiring, grateful servants.
How many times have we seen movies and shows with bad guys who were "created" by a bad system? Loyal government agents turn bad when their child or wife dies as collateral damage. A magnetic X-Man turns into Magneto when he is separated from his parents as a child because of Nazis. And, Agent Smith was given the purpose to eliminate all anomaly within the Matrix system. At the end of M1, Agent Smith found out he couldn't elminate The One. Smith must have known that the only possible way for Neo to survive those gunshots was if the system itself protected him. This would certainly provide some explanation for why Smith seems to want to destroy everything. Or, perhaps he only wishes to finally destroy Neo, and he sees that the only way he can do that is through a complete takeover of the Matrix system so that he can override Neo's death protection.
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