Cryptic crossword clue
Again join sappers company beginning to bore in excavation 9

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

I've seen this crossword clue in Financial Times
R
E
C
O
M
B
I
N
E

Buddy explains!

The straight part
We know that "Again join" is the straight/definition part of the clue. The straight part is often a synonym or definition, in this case again join = recombine.
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 RECOMBINE mean?

RECOMBINE verb
  1. To combine again, especially to reassemble the parts of something previously taken apart in a different manner.
  2. To undergo recombination.

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