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In The Matrix Agent Smith is concerned about Neo and Morpheus getting out of the Matrix. The conversation between agents:

(Rooftop)

Agent Smith: Damn it!

Agent Brown: The trace was completed.

Agent Jones: We have their position.

Agent Brown: The sentinels are standing by.

Agent Jones: Order the strike.

Agent Smith: They're not out yet.

The Matrix transcript (source)

Why is Agent Smith so concerned with killing Neo and Morpheus in the Matrix when a strike on them out of the Matrix would kill them all the same as if they were killed in the Matrix?

Consider that Agent Smith is still an agent of the system (not unplugged) especially when just killing them would be enough.

So what has Agent Smith so riled up that he needs to kill them in the Matrix?

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    I think this is part of Agent Smith's character, he hates Neo, humans, and the Matrix. He wants to get a piece of Neo before someone else does. Similar to the scene where he takes out his ear-piece to tell Morpheus how much he hates humankind and the Matrix. It raises the stakes because its personnel to Agent Smith. – Mark Rogers Feb 3 at 23:03
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    Look, I have one job on this lousy ship. It's stupid, but I'm going to do it, okay? – Mazura Feb 4 at 1:44
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    As a non-english speaker, I always understood that quote to mean that they're not out of trouble yet. Like They may have escaped me, but the sentinels are going to get them. – Martin Véronneau Feb 4 at 13:57
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    @MartinVéronneau, Yeah, I see what you are saying , but when he says They're not out yet. to me it him referring to the fact that they are not out of the Matrix yet. Especially as the other agents say Order the strike which means deploy sentinels and leads to the conclusion that Agent Smith was actually referring to them still being in the Matrix. – KyloRen Feb 6 at 10:50
  • @KyloRen - the point of they're not out yet is that while they're in the Matrix, their ship has to be in an exposed position in order to have a good signal to maintain its connection to the Matrix. The ship can't move without breaking the connection which would kill those still in the Matrix, and thus it is vulnerable to Sentiel attack until they are out. That's why its significant that they're not out yet. He want them dead either way; if he kills them in the Matrix, that's fine; but if not killing them in the real world is easier while they're still connected. – Spudley Feb 6 at 17:19
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The agents do not need to kill Neo, Morpheus, and Trinity in the Matrix -- they can either kill them in the Matrix themselves or order a sentinel strike. Agent Smith is expressing frustration in the quoted lines because it is easier to kill them while they are in the Matrix -- not only can the machines attack them both in the Matrix (with agents) and in the real world (with sentinels), but humans plugged into the Matrix are more vulnerable in the real world because they cannot use EMPs against the sentinels in the real world without killing the humans plugged into the Matrix. Once the humans escape the Matrix the agents cannot attack them, and the sentinels will have to try to kill them while defending against EMPs; moreover, the hovership would be more free to maneuver to escape the sentinels since it would no longer need to stay at broadcast depth.

Agent Smith is also frustrated that Morpheus had escaped capture. The agents had been interrogating Morpheus in order to acquire the access codes to the Zion mainframe (which would allow the machines to more easily destroy Zion). The sentinels could possibly be ordered to capture Morpheus instead of kill him but, again, if Morpheus and his crew have escaped the Matrix then it is much harder for the sentinels to kill them and even more so to capture them. It is much easier to capture Morpheus and his crew while they are still in the Matrix since either the agents can capture them or the sentinels can attempt to capture instead of kill while the hovership is unable to use its EMP.

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    However the Matrix does not want the agents to kill Neo at all as he is created by and for the Matrix. Also while plugged in the 3 can still be captured and tortured for information rather then just killed. – Richard C Feb 3 at 16:18
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    @RichardC I suspect the machines would simply choose another person to be the One if Neo died prematurely. After all, he's not much of a One if he can't survive a few agents. As for capturing Morpheus and his crew, the machines could theoretically capture them with the sentinels in the real world, too -- Agent Smith is expressing frustration that Morpheus has, at that moment, escaped capture. – Null Feb 3 at 16:49
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    @RichardC you are referring to the sequels, which do not exist. Considering the one and only Matrix movie, Neo was not “created by and for the Matrix”, but someone who had just proven to be a serious threat. Even if you consider the hypothetical sequels, there is no sign that these Agents know the meta-plan about Neo. Compare with Why did Agent Johnson try to kill the Key Maker?, they do not seem to know the Architect’s plan, but following their standard procedure, which includes killing Neo. – Holger Feb 4 at 9:33
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    Sorry but the sequels do exist and therefore have to be considered when answering questions. They where sketched out and the main ideas decided on as part of writing the first matrix. It was always intended to be a trilogy and was written as such. Therefore any actions taken by the characters have to consider information we learnt after the event. – Richard C Feb 4 at 12:31
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    @KyloRen Agent Smith lost a golden opportunity to acquire the access codes to the Zion mainframe from a captured hovership captain, which is much better than simply killing him. Wouldn't you be frustrated at the loss of a great opportunity? Agents generally don't show much emotion but they are not completely emotionless -- e.g., Brown and Jones show fear when they run away from Neo, and Agent Smith seems to be a bit more emotional than the others (showing, in particular, anger and hatred). – Null Feb 4 at 14:48
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TLDR

  • Smith does not need or want to kill Morpheus (in the matrix, or the real world); he needs to catch him.
  • Smith is "so riled up" to catch Morpheus because he sees this as his only way out of the matrix.
  • Smith would kill Neo or Trinity to accomplish this, but almost certainly not at the expense of letting Morpheus escape.
  • It is not absolutely clear that the point of the strike would be to kill the humans (at least not Morpheus); it could also be a "plan B" to try and keep Morpheus plugged in.

Reasoning

Like many a good Matrix-universe question, I wasn't sure if there's a direct, succinct, satisfying, explicit canonical answer (disclaimer: the games are a blind spot for me, and I think there are a few comics I haven't seen).

I started with the exchange you quote and worked my way out (without knowing for sure where it would lead), so I'll preserve that process below the rule to show my math.


The script (numbered shooting script, March 29, 1998 -- may differ slightly from actual dialog) has a smidge more context, here:

169 EXT. ROOFTOP - DAY

We rush at the roof access door as it suddenly slams open and the three Agents charge out. But Neo, Trinity and Morpheus are already gone.

AGENT BROWN

The trace was completed.

AGENT JONES

We have their position.

AGENT BROWN

Sentinels are standing by.

AGENT JONES

Order the strike.

Agent Smith can't stand listening to them. He moves to the edge of the building, looking out at the surrounding city.

AGENT SMITH

They're not out yet.

They aren't all unique to this scene, but it suggests a few things:

  • Machines outside the Matrix keep the agents in the loop, presumably via their earpieces.
  • At least in this case, one or more agent has command-control authority over the sentinels. I don't recall if it's clear from the actual scene--either they all have this authority and Jones actually initiates the strike, or Jones is telling Smith, suggesting Smith alone has this authority.
  • Whatever agents are (the consciousness of a machine connected to the matrix? programs? [I'm not sure if there's a "difference" between these...]), we can't safely reason about them as a homogenous group.
  • At minimum, Smith's thinking (and maybe motives) at this point differ from the other agents. They may be diverging, or Smith may be fundamentally different.

Moving beyond this scene, I think we can infer a little bit more. I'll focus on the strike, first:

  • After thinking through it, the machine/agent objective of the sentinel strike is uncertain. The obvious purpose is just seek-and-destroy, but it could also be a last-ditch attempt at keeping Morpheus in the matrix where they can continue trying to break him. Both cases are predicated on reaching ship before everyone is out of the Matrix (or the humans would just use the EMP).
  • The Nebuchadnezzar doesn't detect the sentinels and sound an alarm until scene 181, immediately after Neo kills Smith in the subway station and Smith hops off the train in a new host. In scene 182, Morpheus says they have 5-6 minutes, and the sentinels finally land on the ship in scenes 199/200, while Neo is running up the fire escape.
  • If Jones initiated the strike in scene 169, it took a long time (the entire duration of the subway scene) for the sentinels to get close enough for the hovercraft to detect them plus additional time to reach the ship.
  • If the strike is predicated on reaching the ship before everyone is unplugged, it seems like the sentinels would hold for the order as close to the ship as they can get without being detected.

This seems like reasonable support for seeing the strike as Smith's call, and for assuming that Smith doesn't call the strike until Neo kills him. Let's dig into what Smith might be up to, here.

  • Smith says "They're not out yet" after Jones suggests ordering the strike, but the fact that they aren't out yet probably isn't the reason not to order the strike; the strike would be pointless if they were. I don't think Smith is directly responding to the suggestion.
  • After Jones (presumably) suggested ordering the strike, the script also says "Agent Smith can't stand listening to them". Brown and Jones aren't chattering incessantly, so this reaction is probably about what they're saying and what it means. If the strike is a risky "plan B", proposing it indicates Brown and Jones have rationally concluded it is more likely to succeed than "plan A".

Next, let's turn to the elephant in the room--the subway scene. The next 2 scenes after Smith's statement are worth reading in their entirety:

170 INT. SUBWAY STATION - DAY

An old man sits hunched in the far corner of the station, shadows gathered around him like blankets.

Mumbling, he nurses from a bottle of Thunderbird when -- A PHONE begins to RING. Neo leads Trinity and Morpheus bounding over a set of turnstiles towards the ringing phone inside a graffiti- covered booth.

NEO

Let's go! You first, Morpheus.

Morpheus gets in and answers the phone. Lost in the shadow, the old man watches as Morpheus disappears, the phone dropping, dangling by its cord. His eyes grow wide, glowing white in the dark.

171 EXT. ROOFTOP - DAY

Agent Smith stares, his face twisted with hate. He will never be free of the Matrix. He starts to turn from the edge of the building when he suddenly hears it, his head whipping back around, staring􏰀--

Heh! We actually get a fairly unambiguous clue. Smith's goal up to this point is getting the code from Morpheus, and his motive is freeing himself from the matrix. This suggests:

  • Smith does not actually need or want to kill Morpheus (in the matrix, or the real world); he needs to catch him.
  • Smith would kill Neo or Trinity to accomplish this, but probably not at the expense of missing a chance to re-catch Morpheus.
  • Smith is probably unwilling to order the strike because he's overconfident or in denial about his ability to keep Morpheus from getting out, relative to the risk of losing Morpheus in the strike.

As soon as Morpheus escapes, I think Smith's goal and motive both become vengeance.

Note: The Morpheus interrogation scene is also good reading here--it touches on many of these issues--but I managed to answer the question at hand without working out that far.

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    You don’t need to perform complicated speculations about Smith’s motivation, when he/it tells Morpheus exactly that when interrogating Morpheus without other witnesses. – Holger Feb 4 at 9:41
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    Smith needs to capture Morpheus to escape in film 1. He captures him, breaks him gets the access keys to Zion and then he can be switched off. – Richard C Feb 4 at 14:13
  • @Holger The point of the speculation isn't to divine Smith's motive, but to establish how it squares with the sentinel strike (and, to a lesser degree, his behavior in the subway scene). We wouldn't be having this conversation if the strike was unambiguously contiguous with the motive stated in Smith's monologue. – abathur Feb 5 at 2:52
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If they log into the Matrix, their consciusness 'leaves' the real world, making their bodies "still". That is, "a strike to them out of the Matrix would kill them" is true, but if they weren't in the Matrix they would be able to evade that strike (with an EMP or whatever). In case they were logged to the Matrix, they couldn't 'shoot' an EMP because it would kill all communications hence the 'mental link' of those connected, killing them instantly.

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There are several reasons for this to take place in this way.

In order for Neo to complete his purpose and become the One, allowing the machines to destroy and rebuild Zion, he needs to complete a defined set of actions, one of which involves him being shot in the Matrix and then being "reborn" as the One.

That cannot happen if he is killed by sentinels in the ship too early.

Therefore, this could have been programming that Agent Smith wasn't aware was present that prevented him from giving that strike order. This same programming may have made the sentinels in the ship slow down and delay actually killing the crew members making sure that there was just enough peril to not cause any suspicion but always with the aim of letting Neo re-enter the real world as the one.

Alternatively, this could indicate the start of Smith becoming an independent program, gaining feelings and emotions meaning that he wants to see Neo die at his hand rather then just watch him blink out of existence.

Finally, and I think the main reason he wanted them alive: The main aim of the mission was to get hold of Morpheus to try and unpick his brain and get information. If Morpheus, Trinity and Neo can be caught and reimprisoned, then all the sentinels need to do is kill any free crew members, keeping the 3 trapped in the Matrix for interrogation and removing the ability for the humans to unplug them and kill them. However if the 3 escape the Matrix, then the sentinels can kill them instead as an insurance policy.

Neo: What are they doing to him?

Tank: Breaking into his mind. It’s like hacking into a computer, all it takes is time.

Neo: How much time?

Tank: Depends on the mind. Eventually it will crack and his alpha patterns will change from this to this. When it does, Morpheus will tell them anything they want to know.

Neo: Well, what do they want?

Tank: The leader of every ship is given codes to Zion’s mainframe computer. If an agent got the codes and got into Zion’s mainframe, it could destroy us. We can’t let that happen.

Neo: Trinity?

Tank: Zion’s more important than me or you or even Morpheus.

Neo: Well there has to be something that we can do.

Tank: There is. We pull the plug.

Trinity: You’re going to kill him? Kill Morpheus?

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    Agent Smith did order the sentinel strike. Also, I don't think it's necessary for the One to die and be "reborn" in order to fulfill his purpose -- he only really needs to make the choice to return to the Source. – Null Feb 3 at 15:37
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    Before he was killed the Oracle stated he wasn't the one. Then after he was shot and killed he was. I have always taken that as being the moment the human neo became the one – Richard C Feb 3 at 15:48
  • and Smith ordered the strike once it was clear they where escaping – Richard C Feb 3 at 15:48
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    Neo's death/rebirth is indeed the moment he became the One, but that's not necessarily what caused the previous Ones to become the One. It's just the particular event at which Neo believed he was the One and could fulfill the purpose of the One. Previous Ones could have returned to the Source without dying and being reborn. – Null Feb 3 at 15:56
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    I need to re-watch this. It sounds like Zion just needs an upgrade to their system to use multi-factor authentication and include a way to be notified in case of a potential breach so an existing code can be deactivated. – Michael Richardson Feb 4 at 16:56

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