Pardons in the morning, with nests about that is (9)
I believe the answer is:
amnesties
'pardons' is the definition.
('amnesty' can be a synonym of 'pardon')
'morning with nests about that is' is the wordplay.
'morning' becomes 'am' (as in 12:00 AM).
'with' says to put letters next to each other.
'about' means one lot of letters goes inside another.
'that is' becomes 'ie' (short for Latin 'id est', 'that is').
'nests' going around 'ie' is 'nesties'.
'am'+'nesties'='AMNESTIES'
'in the' is the link.
(Another definition for amnesties that I've seen is " Pardons for people convicted of political offences".)