Burns rot on board ship (9)
I believe the answer is:
smoulders
'burns' is the definition.
(smouldering is a kind of burning)
'rot on board ship' is the wordplay.
'rot' becomes 'moulder' ('moulder' can be a synonym of 'rot').
'on' means one lot of letters goes inside another.
'board ship' becomes 'ss' (I am not sure about this - if you are sure you should believe this answer much more).
'moulder' put into 'ss' is 'SMOULDERS'.
Can you help me to learn more?
(Other definitions for smoulders that I've seen before include "threatens to flare up?" , "Burns slowly without a flame" .)