I got a little inspired and thought it over. Most of the characters in Sly Cooper are rather anthropomorphic yet Clockwerk is just a giant actual owl. Why is that? And I came up with this version.
The Eye of Horus! Possibly the treasure that Cooper's ancestor and Clockwerk fought over and was the one and last treasure Clockwerk ever succeeded in stealing. The gem was imbued with mystical powers that Clockwerk succeeded in unlocking, but turned him into a monster!
Perhaps he kept the gem with him all these years and made it part of his Hate Chip, thus the reason why his parts aged with the destruction of the chip.
This is at best a draft, but I love it none the less. I hope ya'll enjoy it too.