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The transporter technology in Star Trek has been used in many fantastic plot fixes. People are stored in some kind of pattern and rebuilt. This process has been used to cure diseases such as the aging sickness in one Next Generation episode, by reverting to an older pattern.

Has this process ever been used to try to remove implants or Borg nanobots? Are there any known in-universe reasons it would not work?

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As far as I am aware, the transporter has not been used to reverse the full assimilation of a Borg drone.

In the episode in which the aging disease is reversed by the transporter (TNG 2x07 "Unnatural Selection"), they make genetic changes using previously recorded genetic information. This does imply that for this plan to even work, it would only be viable for 4 people where the federation had both physical custody of the assimilated person, and recent transporter data: Picard, Janeway, Tuvok and B'Elanna Torres.

However, the medical personnel are not shown to have any trouble deassimilating any of these people, which would rule out them trying a riskier procedure with the transporter. (Remember that the deaging proceedure was so risky that O'Brien didn't do it: Picard operated the transporter to take responsibility for any mishaps)


Spoilers follow for Star Trek: Picard

Specifically, Season 3. You have been warned.

In Picard season 3, it is revealed that the changelings have infiltrated Starfleet and modified the transporters to change the DNA of people transported to make them able to receive a control signal from the Borg. This signal then takes control of young officers in a kind of assimilation.

After the control signal is neutralised, Admiral Beverly Crusher, as head of Starfleet Medical, comes up with a procedure to reverse this change by the Borg, which is shown on screen as involving the transporter.

Finally, Jack Crusher would be a fifth person who could be listed above as a candidate for having their assimilation reversed in this fashion.

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