Preheat your oven to 425°F. While it heats, prepare your mise en place: mince the garlic fresh (the aroma will be noticeably better than pre-minced), halve the tomatoes lengthwise to help them release their juices during roasting, dice the half onion into small pieces, and zest the lemon. Pat the cod fillets completely dry with paper towels—this ensures they'll cook evenly and develop a better texture.
Lightly oil a 9x13 inch baking dish with 1 tablespoon of olive oil. Arrange the cod fillets in the dish, spacing them evenly. Season both sides of each fillet with salt and pepper, then drizzle with the remaining 1 tablespoon of olive oil and top with the lemon zest. I like to add the zest at this stage so it infuses into the fish as it cooks rather than sitting on top of the sauce.
In a bowl, combine the halved tomatoes, kalamata olives, diced onion, and minced garlic from Step 1. Add the remaining 2 tablespoons of olive oil, red wine vinegar, dried oregano, salt, and red pepper flakes. Stir gently to combine, letting the acidity of the vinegar and brightness of the oregano begin to develop. The mixture should feel balanced—not too oily, not too acidic.
Distribute the Mediterranean topping from Step 3 evenly over the seasoned cod fillets, making sure each fillet gets a generous portion of tomatoes, olives, and aromatics. Slide the dish into the preheated 425°F oven and bake for 15-18 minutes until the fish reaches an internal temperature of 140°F at its thickest point. The cod should be opaque and flake easily with a fork.
Remove the baking dish from the oven and let it rest for 2 minutes. Transfer each cod fillet to a serving plate or platter, spooning the tomato-olive mixture and accumulated pan juices over the top. Garnish generously with fresh parsley and serve immediately with lemon wedges on the side for extra brightness.