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It's a quote from the TV drama Manifest. Here are the lines:

-Per protocol, climbing to penetration altitude.
-Per protocol, adjusting flight path to storm center.

The drama is about a bunch of passengers and crew of a commercial airliner who suddenly reappear after being presumed dead for over five years.

The plane captain as the speaker of this line is trying to fly up to the sky and looking for some dark lightning to prove his own theory. What confused me is the meaning of per protocol. It seems like a regular term of airplane.

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Taking into account that

protocol

The accepted or established code of procedure or behaviour in any group, organization, or situation.

and that

per

by means of

we can infer that per protocol means that the captain is using the established protocol, he is following the steps clearly defined in such protocol, the set of mandatory steps that he must execute on facing an specific situation, an emergency. He declares aloud each step, that he's always following the rules, because what he says is being recorded in the black box of the plane. In case of accident these records will help to determine the causes, what went wrong.

@Tᴚoɯɐuo suggested that per protocol can be paraphrased as according to / in accord with protocol.

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    +1 for the explanation, but per protocol isn't a truncated form of "as per protocol"; rather "as per protocol" is just a variant.
    – TimR
    Jan 15, 2019 at 11:12
  • @Tᴚoɯɐuo Then in this case, "per" means just "by means of", isn't it?
    – RubioRic
    Jan 15, 2019 at 11:19
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    I would paraphrase it as "according to" or "in accord with".
    – TimR
    Jan 15, 2019 at 11:20

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