Stop to get a container to put the second in (5)
I believe the answer is:
avast
'stop' is the definition.
(I've seen this before)
'a container to put the second in' is the wordplay.
'container' becomes 'vat' (vat is a kind of container).
'to put' is a charade indicator (letters next to each other).
'the second' becomes 's' (common abbreviation).
'in' indicates putting letters inside.
'a'+'vat'='avat'
'avat' placed around 's' is 'AVAST'.
'to get' is the link.
(Other definitions for avast that I've seen before include "Stop, nautically speaking" , "Stop on board" , "Stop! (naut.)" , "order for tar" , "Stop (nautical)" .)