Yes, that was to be mentioned in the later parts of the scripting section. Need to get my rear around to finishing that.
Basically, you can not pause the environment around the player. You can however setposition, spawn and delete things however you wish. Using the scene transitions such as black out and black in, or creatively positioning the camera so that the viewer can't see things happening beyond the screen edge, you can manipulate the environment easy enough. You'll first want to setcaptive the player so that the enemy does not view him as a target. Then remove control from him so he can't shoot himself in the foot or other lethal action. You can grab the coordinates, speed, direction of any units or objects you wish as the scene begins and then reposition things where you need them as it closes but this would remove from the realism.
The most popular cutscene protocol is to player setcaptive true/false and enableuserinput false/true. The rest of the ambience should be left alone to add life to the background. Does that clear anything at all up?