Penetration focuses on two individuals, a father and daughter. The natural world around them takes on the role of a third character called the Mothering Earth. Whenever you move the mouse pointer over a link, the status bar at the bottom of the window indicates which character the link leads to.

Links leading to unvisited nodes (that is, sections of text not yet read) are white, while dark green links indicate nodes that you have already visited. A shade of light green (lying between the other two link colors) signifies that you have visited the node but it has not been fully revealed to you. If you click on a light green link to return to one of these partially revealed nodes, you will find the node's contents altered to reflect the new context in which you are reading it. This is accomplished by means of variable text elements created with the Connection System.