Season the fish. Preheat an oven to 400°F (205°C). Pat the cod filets dry on all sides with paper towels, then season on all sides with Kosher salt and freshly ground black pepper. Set aside to come to room temperature.
Sauté the aromatics. Heat 2 Tbsp olive oil in a large skillet over medium-high heat. When hot, add diced onion. Season with ½ tsp Kosher salt then cook, stirring occasionally until softened, about 4-6 minutes. Add 2 cloves grated garlic, ½ tsp fennel seeds, and ¼ tsp crushed red pepper flakes, then cook 1 minute more.
Make the cherry tomato sauce. Add 2 pints of cherry tomatoes, season with ½ tsp Kosher salt, then cook, stirring occasionally, until the tomatoes begin to burst, about 8-10 minutes. Add in 1 can of butter beans (along with the liquid) and stir well.
Mix the topping. In a mixing bowl, whisk together ⅓ cup seasoned breadcrumbs, ¼ cup grated Parmesan, 2 tsp chopped oregano, 2 tsp fresh lemon zest, and a generous pinch of Kosher salt. Stir in 2-3 Tbsp extra virgin olive oil, until the breadcrumb mixture is moistened.
Coat in breadcrumbs. Press one side of each cod filet firmly into the breadcrumbs, then nestle into the cherry tomato sauce, topping side up. Repeat with remaining cod pieces.
Bake the cod fish. Transfer to a preheated oven and cook for 12-15 minutes, or until the cook is fully cooked through and the internal temperature is 140-145°F (60-63°C). Garnish with additional fresh oregano and a pinch of flaky sea salt, then serve with lemon wedges. Enjoy!