Place a small pan over medium-high heat until hot , coated with nonstick cooking spray. Add mushrooms, salt, and pepper. Coat the mushrooms with more nonstick spray and cook until soft (about 4 minutes), stirring frequently.
Add the onions and cook for another minute, then set the skillet aside.
Place another small pan over medium heat until hot. Coat with the nonstick cooking spray, then add the egg substitute and cook without stirring for 1 minute. Using a rubber spatula, lift up the edges to allow the uncooked mixture to run underneath.
Cook 1-2 minutes longer or until the eggs are nearly set. They will begin to puff up slightly.
Spoon the mushroom mixture on one half of the omelet. Sprinkle the cheese over the mushrooms evenly and then use the spatula to fold the omelet over the mushrooms and cheese. Cut in half and serve.