Every second, a flier's coming in behind schedule (9)
I believe the answer is:
Here is my best explanation:
'every second' is the definition.
('alternate' can be a synonym of 'every second')
'a flier's coming in behind schedule' is the subsidiary indication.
'flier' becomes 'tern' (tern is a kind of birdanimal**).
'coming in' means one lot of letters goes inside another.
'behind schedule' becomes 'late' (I've seen this in other clues).
'tern' inserted inside 'late' is 'lternate'.
(Other definitions for alternate that I've seen before include "Change from one thing to another by turns", "Happen in turns, rotate", "Happening or following in turns, one after the other", "Do in turn repeatedly", "Go in turns", "Act reciprocally", "Occur in turn repeatedly", "Take turns", "Change repeatedly between two" and "First the one, then the other".)