Ship stores fish in jars (6)
I believe the answer is:
shakes
'jars' is the definition.
(I've seen this before)
'ship stores fish' is the wordplay.
'ship' becomes 'ss'.
'stores' means one lot of letters goes inside another.
'fish' becomes 'hake' (I've seen this before**).
'ss' placed around 'hake' is 'SHAKES'.
'in' is the link.
(Other definitions for shakes that I've seen before include "Judders" , "Quivers" , "Moves quickly up and down, say milk drink" , "jars" , "Frothy drink of milk and flavouring" .)