Submarine rises to the top of the sea and heads for shelters at various stages (3,5)
I believe the answer is:
bus stops
'various stages' is the definition.
Although both the answer and definition are plural nouns, I cannot see how one could define the other.
'submarine rises to the top of the sea and heads for shelters' is the wordplay.
'submarine' becomes 'sub' ('sub' can be a synonym of 'submarine').
'rises' shows that the letters should be reversed in order.
'to the top of the sea' becomes 'stop' (I can't explain this - if you can you should give a lot more credence to this answer).
'and' is a charade indicator (letters next to each other).
'heads for' indicates taking the first letters (I've seen 'head for' mean this).
The first letter of 'shelters' is 's'.
'sub' reversed gives 'bus'.
'bus'+'stop'+'s'='BUS STOPS'
'at' is the link.
Can you help me to learn more?
(Other definitions for bus stops that I've seen before include "Points at which to pick up and put down passengers" , "Where folk queue in street" .)