... the essential message comes at the end of it! (6,4)
I believe the answer is:
bottom line
'the essential message' is the definition.
'bottom line' can be an answer for 'message' (bottom line is a kind of message). I am not sure about the 'the essential' bit.
'at the end of it' is the wordplay.
I cannot quite see how this works, but
'at' could be 'in' (synonymous in some cases - eg at school, in school) and 'in' is located in the answer.
'of' could be 'o' and 'o' is found in the answer.
'it' could be 't' (abbreviation. e.g. in 'tis) and 't' is located in the answer.
This explanation may well be incorrect...
'comes' is the link.
Can you help me to learn more?
(Other definitions for bottom line that I've seen before include "Fundamental factor" , "The basic reality of a situation" , "deciding factor" , "Fundamental aspect of a situation" , "Essential point (for an accountant?)" .)