The Capture, by Kathryn Lasky, was published in 2003 by Scholastic.
Pushed from his family’s nest by his older brother, barn owl Soren is rescued from certain death on the forest floor by agents from a mysterious school for orphaned owls, St. Aggie’s. With new friend, clever and scrappy Gylfie, he uncovers is a training camp for the leader’s own nefarious goal.
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I always wanted to read this and never did! I had no idea it was set in a post-human world, though! I thought it was just about talking owls!