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When Smith assimilated Bane, why didn't the operators in Zion notice the code change (which I assume one would have to be watching the screens)? I would guess each individual has their own unique code, as operators seem to read where certain people are at any given time.

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    Because they can't tell much beyond blonde, redhead, brunette? – Broklynite Dec 16 '16 at 13:03
  • @Broklynite cool stuff, but seriously though... >__> – Cake_Badger Dec 16 '16 at 13:26
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    Wasn't more than one person trying to get out? Operator setting up the extraction call? Physically helping someone else get disconnected? Could be anything. That's presuming too, that if they saw it they would know what happened - they don't seem to see much beyond "something went wacky", and this would definitely be something they had never seen before. – Radhil Dec 16 '16 at 13:34
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    Just my take, but I'm guessing the idea of an Agent hijacking a human mind in the Real World (tm) was just as farfetched to the operators as it was to everyone Smith proceeded to ambush. It's something that has never happened before. They may have noticed "something odd" but wrote it off as a glitch. They almost certainly would not have jumped to the conclusion "an Agent is taking over his mind! Stop him!" – Steve-O Dec 16 '16 at 14:55
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    This is a good question and deserves more upvotes. – Null Dec 16 '16 at 22:20
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At the time that Smith assimilated Bane, all the Zion hoverships had been ordered to return to Zion by Commander Lock. Only one ship, the Caduceus, remained at broadcast level, and only because its captain (Ballard) agreed to defy Commander Lock's order and wait for a message from the Oracle. Consequently, only one operator could have been monitoring the Matrix when Smith assimilated Bane. Furthermore, that operator wouldn't have recognized Smith's code because Smith was no longer an Agent.1 The operator would have had a small window of time to notice something weird happening to Bane between the start of Bane's assimilation until Bane-Smith jacked out, but that window lasted only about thirty seconds.2 The operator evidently was not paying attention to the Matrix feed of Bane during that small window, otherwise he would have ended the phone call before Bane-Smith could jack out. There are several possible reasons why the operator was not paying attention:

  • The operator was probably helping Malachi (the operative who jacked out just before Bane) remove his head jack in the real world. Someone in the real world usually helps a person remove his head jack (e.g. Tank helped Neo and Dozer helped Morpheus remove their head jacks after the jump training program in The Matrix). The operator would have been the only one able to help Malachi if all the other crew members were still jacked into the Matrix.
  • The operator may have been busy helping other crew members in the Matrix at the time (e.g. finding an exit, giving directions to run away from an Agent, loading equipment, etc.).
  • The operator may have been watching for Sentinels in the real world. One of the captains at the Crisis Meeting mentioned that the Sentinels had recently made it more difficult to hack into the Matrix, so Sentinels would have been a serious threat.

1 Link, the operator of Morpheus' hovership, did not recognize Smith's code earlier in the film, when Smith appeared at the Crisis Meeting:

Morpheus: What happened back there, Link?

Link: I can’t figure it out, sir. Agents just came out of nowhere. And then the code got all weird. Encryption I’ve never seen.

The Matrix Reloaded transcript (source)

2 See the window of time for yourself:

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