Cryptic crossword clue
Run through quaggy peat, otherwise enter therein 9

The most common and most likely answer to this crossword clue is the 9 letter word PENETRATE

P
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Buddy explains!

The straight part
We know that "Run through" is the straight/definition part of the clue. The straight part is often a synonym or definition, in this case run through = penetrate.
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 PENETRATE mean?

PENETRATE verb
  1. To enter into; to make way into the interior of; to pierce.
  2. To achieve understanding of, despite some obstacle; to comprehend; to understand.
  3. To affect profoundly through the senses or feelings; to move deeply.
  4. To infiltrate an enemy to gather intelligence.
  5. To insert the penis into an opening, such as a vagina or anus.
  6. To move a piece past the defending pieces of one's opponent.

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