In a manner, homing pigeons go by it (3)
I believe the answer is:
air
'in' is the definition.
The definition and answer can be both substances as well as being singular nouns.
Maybe you can see a link between them that I don't see?
I cannot understand how the rest of the clue works.
Can you help me to learn more?
(Other definitions for air that I've seen before include "Short song" , "The earth's atmosphere" , "Broadcast; mien" , "Tune (on the G string?)" , "Space above and around" .)