The low power trigger pulse is sent out by the commander while the shutter is open. Its function is to tell all of the remotes to "Fire Now" for image capture. It will occur right after the shutter opens, unless you are in rear curtain sync mode, in which case it will occur just prior to shutter closing.
As Russ indicated, the trigger pulse is very low power and will contribute to the exposure if the subject is quite close to the camera. If this is a problem, obtain a Nikon SG-3IR (about $12 or so) and place it in the camera's hot shoe. The small filter goes in front of the popup flash and absorbs the visible component of the preflash and trigger pulses, while passing the InfraRed (IR) component that the remote speedlights are looking for.
HBB in Phoenix, Arizona Nikonian Team Member
Photography is a journey with no conceivable destination.