To Royal Navy trouble is whirlwind (7)
I believe the answer is:
tornado
'whirlwind' is the definition.
(I've seen this before)
'to royal navy trouble' is the wordplay.
'royal navy' becomes 'RN' (abbreviation for Royal Navy).
'trouble' becomes 'ado' (both can mean bother or commotion).
'to'+'rn'+'ado'='TORNADO'
'is' is the link.
(Other definitions for tornado that I've seen before include "Major storm" , "Violent wind vortex" , "Funnelling wind" , "Type of cyclone" , "Violent swirling wind" .)