For Crust: Stir water, sugar and yeast together until dissolved. Add the olive oil and the salt. Stir in the flour until well blended. Let dough rise for an hour.
For Sauce: Mix tomatoes, tomato sauce, onion, garlic, salt, pepper, oregano, basil, bay leaf and sugar in a saucepan. Simmer for 30 minutes or longer.
Pizza: Preheat oven to 425 degrees.
Spray Pam or another cooking spray on a 9 inch round baking dish.
Split whole-wheat dough into two sections, one section larger than the other. Roll out larger (about 1/4 inch thick) section and place in round baking dish. Leave about 1 inch hanging over the sides.
Roll out smaller dough section (1/4 inch thick) and reserve for the top.
Fill crust in dish with topping: green pepper, pepperoni, onion, mushrooms, and any other toppings desired. Use enough toppings to fill the dish 3/4 the way full, leave room for the sauce. Top with Mozzarella cheese.
Pour sauce over the top of vegetables. (Depending on topping all the sauce may not fit in dish.).
Place remaining crust over the sauce, cheese and topping mixture.
Trim to fit the shape of the 9-inch dish. Pinch sides together with bottom crust.
Cut slits in top to create air vents.
Cook covered with foil for 20 minutes. Remove foil and cook the rest of the way till crust on top is brown and center is warm.
Cut into pie piece shape and serve. (You may have remaining liquid at bottom from vegetables, just spoon out into sink to prevent the crust from getting soggy.).