It turns out I'm 7 years late seeing this, still I couldn't help but share it. 'The Bronson Maneuver' is a short animation created by a small group for a challenge ran by cgsociety.org. It needed to fill the theme of Secret Agent and it does just that.
It's a great piece that combines stopmotion characters with 2D backgrounds, all composited in After Effects. If you keep watching you can see some 'making of' clips.