When you point at a duck and pull the trigger, the computer in the NES blacks out the screen and the Zapper diode begins reception. Then, the computer flashes a solid white block around the targets you’re supposed to be shooting at. The photodiode in the Zapper detects the change in light intensity and tells the computer that it’s pointed at a lit target block — in others words, you should get a point because you hit a target. In the event of multiple targets, a white block is drawn around each potential target one at a time. The diode’s reception of light combined with the sequence of the drawing of the targets lets the computer know that you hit a target and which one it was. Of course, when you’re playing the game, you don’t notice the blackout and the targets flashing because it all happens in a fraction of a second.
Source: How Did The Nintendo Duckhunter Gun Work?
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