I've never had a deep-dish pizza in Chicago, unfortunately, but I am a huge Chicago Bears fan & wanted to make something in the spirit of the town for my games. I researched authentic Chicago deep-dish pizzas & came up w/ my own version, that even my Philly Eagles' fan teenage son thinks is da best.
Press pizza dough in 9 x 13" pan, including up along the sides. (Depending type of dough, make sure to spray w/ cooking spray 1st.) Bake dough according to directions.
Add some olive oil (abt 1-2 Tbs) to a skillet & heat. Remove casings from sausage & crumble. Fry until a golden brown. Remove sausage & sprinkle over pizza crust evenly. Sprinkle mozzarella all over the sausage & pizza crust. Layer pepperoni on top.
Sautee onions, mushrooms, & green pepper until tender. Drain juices. Add tomatoes, spices, (except for fresh parsley) & simmer all together. NOTE: Fennel seed is delicious, but strong -- you don't need much. Add splash of red wine & fresh parsley. Simmer a bit more. When cooked just enough, spoon over the mozzarella, covering the entire pizza.
Top with freshly grated parmesan reggiano. Bake at 350 degrees for about 30 minutes. Enjoy! This even tastes good straight from the refrigerator the next day cold.