The weed having to taxi over with Commanding Officer (7)
I believe the answer is:
tobacco
'the weed' is the definition.
(I've seen this before)
'to taxi over with commanding officer' is the wordplay.
'taxi' becomes 'cab' ('cab' can be a synonym of 'taxi').
'over' says the letters should be written in reverse.
'with' says to put letters next to each other.
'commanding officer' becomes 'co'.
'cab' backwards is 'bac'.
'to'+'bac'+'co'='TOBACCO'
'having' acts as a link.
(Other definitions for tobacco that I've seen before include "Leaves to smoke" , "Smoked narcotic plant" , "Eg, shag or snuff" , "Smoker's leaf" , "Narcotic leaf plant" .)