Whatever his rank, he's the captain (5)

I believe the answer is:

pilot

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'captain' is the definition.
(thesaurus)

I don't understand how the remainder of the clue works.

(Other definitions for pilot that I've seen before include "air traffic controller?" , "Plane's operator" , "may be up in the clouds" , "Name of Mr Rochester's dog" , "Airman" .)

I've seen this clue in the Evening Standard.

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