The most common and most likely answer to this crossword clue is the 4 letter word ANUS
A
N
U
S
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The straight part
We know that "waste passage ends here" is the straight/definition part of the clue. The straight part is often a synonym or definition, in this case waste passage ends here = anus.The cryptic/wordplay part
In cryptic crossword there's often an wordplay/cryptic part as well.This part involves a more complex hint, such as an anagram, homophone, hidden word, etc.
Sadly, We don't have an explanation for this specific crossword clue yet.
What does ANUS mean?
ANUS noun- The lower orifice of the alimentary canal, through which feces and flatus are ejected.