Captain is not prepared to tackle the onset of such a state of commotion (5,8)
I believe the answer is:
panic stations
'a state of commotion' is the definition.
(informal term for a state of panic)
'captain is not prepared to tackle the onset of such' is the wordplay.
'prepared' indicates anagramming the letters.
'to tackle' indicates putting letters inside (tackle can mean to take hold of).
'the onset of' suggests taking the first letters.
The first letter of 'such' is 's'.
'captain'+'is'+'not'='captainisnot'
'captainisnot' with letters rearranged gives 'panictations'.
'panictations' placed around 's' is 'PANIC STATIONS'.
(Other definitions for panic stations that I've seen before include "indicating emergency" , "(Humorous) alarm call" , "Where everyone is scared and frenetic" , "state of emergency" , "State of alarm (colloq.)" .)