Agitated microbiologist — no stoic — creates confusion (9)
I believe the answer is:
imbroglio
'confusion' is the definition.
(I've seen this before)
'agitated microbiologist no stoic' is the wordplay.
'agitated' indicates an anagram.
'no' indicates named letters should be taken away.
'microbiologist' with 'stoic' removed is 'mrbiologi'.
'mrbiologi' is an anagram of 'IMBROGLIO'.
'creates' is the link.
(Other definitions for imbroglio that I've seen before include "Confused mess" , "Dilemma" , "Jumble" , "Complicated situation" , "Confused situation results" .)