When back, the shipper disposed of the gems (9)
I believe the answer is:
sapphires
'the gems' is the definition.
(sapphire is a kind of gem)
'when back the shipper disposed' is the wordplay.
'when' becomes 'as' (eg 'when I walked' means 'as I walked').
'back' says the letters should be written in reverse.
'disposed' indicates anagramming the letters.
'as' back-to-front is 'sa'.
'shipper' anagrammed gives 'pphires'.
'sa'+'pphires'='SAPPHIRES'
'of' acts as a link.
(Other definitions for sapphires that I've seen before include "precious stones" , "Blue gems" .)