"Stopping down" mean making the aperture smaller.
For example: f/2 is a larger aperture; f/8 is a smaller aperture. It is smaller by 4-f/stops (f/2.8, f/4, f/5.6, f/8). To go from f/2 to f/8 means you are "stopping down" the aperture by 4 stops.
The term "stop" comes from the old design of lenses where the area of the aperture was controlled by a rotating ring that had click "stops" for setting the aperture. Each click let in twice as much or half as much light depending on which direction you went. Light is proportional to area. f/stops are give in diameters of the aperture to the focal length of the lens. Area has a squared relationship to diameter.