Highest in command initially skirts the issues (6)
I believe the answer is:
topics
'the issues' is the definition.
('topic' can be a synonym of 'issue')
'highest in command initially skirts' is the wordplay.
'highest' becomes 'top' (at the top).
'in command' becomes 'ic' (military abbreviation).
'initially' indicates taking the first letters.
The first letter of 'skirts' is 's'.
'top'+'ic'+'s'='TOPICS'
(Other definitions for topics that I've seen before include "Subject matter of conversations" , "Subjects to talk about" , "Subject matters" , "Talking points" , "Subjects under discussion" .)