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Based on the episode The Wounded a Starfleet captain has access to prefix numbers that allow a captain to remotely lower the shields of another Starfleet vessel, even when the legitimate captain is still in command of the other vessel.

Based on this popular answer an admiral might be needed to gain access to a ship's prefix number. This doesn't seem to make sense though because in Paradise Lost, Admiral Leyton orders the USS Lakota to destroy the USS Defiant but they don't get any prefix number.

Other examples:

  • The Starfleet fleet vs the USS Prometheus.
  • The Starfleet fleet vs the Enterprise when the M5 took over.
  • In Star Trek Insurrection when the Admiral grudgingly tells the Sona they can fire on the Enterprise E to stop them.

Why wouldn't Starfleet vessels always lower each other's shields when they fight?

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In "The Wounded", it wasn't Starfleet who used the prefix code, but the Cardassians after Picard gave it to them when the Enterprise couldn't get to the battle in time. The simplest explanation is that Maxwell was caught by surprise that the Cardassians would have the code in the first place and so was unprepared for the tactic. Note that the trick didn't work twice when Enterprise is preparing to fight the Phoenix and the latter had its shields up, and it wasn't even suggested trying.

As for why it isn't used all the time in Starfleet v Starfleet fights is that in that case the opponents know the other side has access to the codes and would take action to prevent it being used in preparation for battle. The first time it's seen in The Wrath of Khan, it's explicitly stated it's a longshot and implies that if it does work it's because Khan and his crew are not familiar enough with Starfleet tech and don't realize it's possible.

Spock: Assuming he hasn't changed the combination. He is quite intelligent.

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    The only (potential) fly in your answer is the episode Peak Performance. Worf uses the "Entperise's security override" to fool the sensors during a war game. – Xantec Sep 20 '18 at 15:16
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    Actually, in that episode Worf cheated by using his security codes. However, it was allowed as it was attributed to "Klingon guile" and the fact that enemies don't always play by the rules. Therefore, I think the answer is ok as it is, even though some quotes to support it would be nice – Rebel-Scum Sep 20 '18 at 15:28
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    @Xantec: Worf is the chief security officer of the ship he is tricking. I don't think that's a loophole. It's not surprising that the sysadmin of your own system can mess with it even when he's offsite. Especially considering he wasn't "compromised" and the Enteprise didn't expect to need to take any such precaution. – ThePopMachine Sep 20 '18 at 15:29
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    @Xantec There's no indication that's the prefix code in use, though. More likely it's simply Worf using his security codes to spoof legitimate sensor data. Because the computer expects to receive sensor data, it's not the red-flag, alert-the-crew moment that an actual override command is. (Note that Worf doesn't try a more direct form of sabotage such as, indeed, lowering the shields.) – Cadence Sep 20 '18 at 15:42
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First of all, StarFleet ship fighting StarFleet ship is an exceedingly rare occurrence in universe and, the fight between the Defiant and the Lakota aside, always a result of a crew being subdued or manipulated or a ship being commandeered in some way. Alien entity taking control of crew and/or ship, mad computer, etc...

The short-lived battle between the Lakota and the Defiant is the only known occurrence of a fight between two StarFleet vessels manned by StarFleet crews that were not under some sort of alien influence. Although the crew of the Lakota acted under false information provided by Admiral Leyton, even though Captain Benteen knew the truth as she was part of the conspiracy.

Since, as shown in Wrath of Khan, an override to the use of the prefix code exist, it seems logical that two StarFleet ships manned by StarFleet crew fighting each other would activate that override before the fight begins, to avoid their opponent using it against them, thus making this action useless. Thus why Benteen or Worf didn't even attempted to use it.

From what little we hear and see about it on screen, it seems that the prefix code is a measure designed to retake a ship that has fallen into the hands of someone else than the Federation. It would be quite improbable that those people wouldn't know about the prefix code, since it seems to be known only by the upper echelons of the hierarchy, thus giving a major advantage to the recovery crew, allowing them to control the commandeered ship at a distance and avoid loss off life when they beam in to effectively retake command of the ship.

It would also seem that the prefix codes are available only to the Admiralty: Kirk was Admiral when he fought the Reliant under orders of Khan, and Picard had to call an Admiral at StarFleet Command before he was given the prefix code of the Phoenix.

It would be logical that, for security reasons, prefix codes are held in a secure computer memory somewhere at StarFleet Command, and not stored in the memory banks of every StarFleet vessels, to avoid an enemy obtaining them when they capture one ship, or even comb through the wreckage of a destroyed StarFleet ship.

It would also explain why, in Insurrection, Admiral Dougherty doesn't give the Enterprise's prefix code to the Sona: the Briar Patch was preventing communication with StarFleet, and it is doubtful that the Admiral would have carried the information with him on the Sona ship for security reasons. It's not the kind of information that you would transmit to a ship of another organization, even an ally, or transport in a briefcase.

As for the fight against the Prometheus, since we do not see or hear the crews of the StarFleet fleet during the short battle, we cannot know if they tried it or not. Given the efficiency of the Tal Shiar, the Romulan Secret Service, it is conceivable that they managed to learn about the prefix code and its override, and that they activated the override beforehand. We do not know enough about what led to the events seen in the episode to be able to draw a conclusion.

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    The use of the word "overtaken" in the first paragraph to mean "possessed" or "mind controlled" is quite unusual. I doubt that Kirk carried around a computer disc with the prefix codes of tens, hundreds, or thousands of starships in WOK. In WOK Kirk orders the bridge cleared, perhaps to keep the secret known to the bare minimum of people, and then orders Saavik to: "punch up the data charts of the Reliant's command console", implying that is a little used file in the computer. We don't see Kirk insert a data file into the system, and Spock knows about Prefix codes. – M. A. Golding Sep 20 '18 at 17:51
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    My apologizes, I'm not a native English speaker, sometimes I mix words. I have edited 'overtaken' and replaced it by what I hope is a more clear sentence. You are right about what we see on screen in WOK. But there can be many explanations as to why Spock knows about it and the file being in the Enterprise databanks: Spock may have seen it in use before, the files may have been automatically uploaded before Kirk stepped foot on the ship, since his presence was planned, or when he assumed command and replaced Spock as CO of the ship. We do not know enough to be sure. – Sava Sep 20 '18 at 18:10
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    FWIW, "overtaken" was just fine. – Lightness Races in Orbit May 28 at 10:16

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