Crossword Genius

Breaking down, how come? (4,2)

Ross

I believe the answer is:

show up

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'come?' is the definition.
(thesaurus)

'breaking down how' is the wordplay.
'breaking' means one lot of letters goes inside another.
'down' becomes 'sup' (I can't explain this - if you can you should believe this answer much more).
'sup' enclosing 'how' is 'SHOW UP'.

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(Other definitions for show up that I've seen before include "Become visible" , "Arrive - put to shame" , "Make an appearance" , "Put in appearance or expose" , "Expose or keep appointment" .)

I've seen this clue in The Times and The Sunday Times.
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