If you're in gear in a car and not accelerating, the car slows down faster than it would from just air resistance and tire deformation. In normal braking, the energy is turned into heat from the brake pad rubbing on something connected to the tire. Where does your car's kinetic energy go when engine braking? IE how does energy get transferred between the road and the car to remove the car's kinetic energy?
The wikipedia article on this doesn't seem to explain it, and google searching didn't turn up anything enlightening.