Top archaeologist was taken aback by the excavation in general (2,1,5)
I believe the answer is:
as a whole
'in general' is the definition.
(synonyms)
'top archaeologist was taken aback by the excavation' is the wordplay.
'top' indicates taking the first letters (in a down clue, the first letter is top).
'taken aback' says the letters should be written backwards.
'by' means one lot of letters go next to another.
'the excavation' becomes 'hole' (I've seen this before).
The first letter of 'archaeologist' is 'a'.
'was' back-to-front is 'saw'.
'a'+'saw'+'hole'='AS A WHOLE'
(Other definitions for as a whole that I've seen before include "completely" , "In general" .)