Cut eggplant into cubes. Sprinkle with salt and let sit in a colander for 20 minutes. Press out excess liquid.
Heat oil in large pot over medium-high heat. Add anchovies and let melt in oil, stirring frequently. Add fennel and saute until browned and caramelized about 5-7 minutes. Add eggplant, garlic and bell peppers and season with salt and pepper. Cover and sweat out the vegetables, about 5-6 minutes, cooking until the eggplant becomes to brown.
Add tomatoes, stirring to combine. Bring to a boil then reduce heat to medium-low. Simmer for 15 minutes, stirring occasionally. Stir in torn basil and season sauce with salt and pepper.
Meanwhile, cook pasta according to directions on package. Drain cooked pasta, reserving ¼ cup of the pasta water.
Heat large saute pan over medium-high heat. Add the cooked rigatoni, spoon the sauce on top and pour in the reserved pasta water. Stir until pasta is well coated with the sauce. Plate onto 4 bowls. Grate parmesan on top and serve.