Assemble in the mother ship (4)
I believe the answer is:
mass
'assemble' is the definition.
(thesaurus)
'mother ship' is the wordplay.
'mother' becomes 'ma' (ma is a kind of mother).
'ship' becomes 'ss'.
'ma'+'ss'='MASS'
'in the' acts as a link.
(Other definitions for mass that I've seen before include "Ceremony for many" , "Quantity; religious service" , "Religious celebration" , "what 13 15A [STANDARD MODEL] supposes 12 [HIGGS BOSON] gives other 5A [PARTICLES]s" , "Pound, maybe" .)