Captain altered course in fit of severe anxiety (5,6)
I believe the answer is:
panic attack
'fit of severe anxiety' is the definition.
(sudden episode of anxiety)
'captain altered course' is the wordplay.
'altered' is an anagram indicator.
'course' becomes 'tack' (I've seen this before).
'captain' anagrammed gives 'panicat'.
'panicat'+'tack'='PANIC ATTACK'
'in' acts as a link.
(Other definitions for panic attack that I've seen before include "terribly anxious spell" , "Sudden overwhelming anxiety" , "Sudden fear" .)