Meteorological phenomenon commander took in, in leaving war zone (8,5)
I believe the answer is:
occluded front
'meteorological phenomenon' is the definition.
(type of weather front)
'commander took in in leaving war zone' is the wordplay.
'commander' becomes 'oc' (I've seen this in other clues).
'took in' becomes 'included'.
'leaving' suggests deleting specific letters.
'war zone' becomes 'front' (area where a war is being fought).
'included' with 'in' removed is 'cluded'.
'oc'+'cluded'+'front'='OCCLUDED FRONT'
(Another definition for occluded front that I've seen is " Weather-map feature".)