All 4 Uses

comprehend
in
The Secret Sharer
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I. On my right hand there were lines of fishing stakes resembling a mysterious system of half-submerged bamboo fences, incomprehensible in its division of the domain of tropical fishes, and crazy of aspect as if abandoned forever by some nomad tribe of fishermen now gone to the other end of the ocean; for there was no sign of human habitation as far as the eye could reach.†

incomprehensible = not understandable

standard prefix: The prefix "in-" in incomprehensible means not and reverses the meaning of comprehensible. This is the same pattern you see in words like invisible, incomplete, and insecure.
His obscure tenacity on that point had in it something incomprehensible and a little awful; something, as it were, mystical, quite apart from his anxiety that he should not be suspected of "countenancing any doings of that sort."†
*
It was this maddening course of being shouted at, checked without rhyme or reason, arbitrarily chased out of my cabin, suddenly called into it, sent flying out of his pantry on incomprehensible errands, that accounted for the growing wretchedness of his expression.†
He actually had the impudence, or else so forgot himself in his wonder at such an incomprehensible order, as to repeat: "Open the quarter-deck ports!†

Definitions:

(1) (comprehend)
to understand something -- especially to understand it completely
(2) (meaning too rare to warrant focus)
Much more rarely (and more frequently in the past), comprehend can mean to include as part of something broader. That was the first sense of the word listed in Webster's Dictionary of 1828 with this sample sentence: "The empire of Great Britain comprehends England, Scotland and Ireland, with their dependencies."