Preheat your oven to 375°F and position the rack to the middle of the oven. While it heats, prepare all your ingredients: slice the mushrooms into 1/4-inch pieces, dice the bell peppers into 1/2-inch pieces, and chop the green onions (using white and light green parts only). Having everything prepped before you start cooking ensures a smooth workflow and prevents any ingredients from being overcooked while you're still preparing others.
Heat the melted butter in a large skillet over medium-high heat. Add the sliced mushrooms first and cook for 4-5 minutes, stirring occasionally, until they begin to release their moisture and lightly brown. Add the diced bell peppers and continue cooking for another 3-4 minutes until the peppers are softened but still have some texture. Season generously with salt and freshly ground black pepper as you cook—this is when you build the foundation of flavor for the entire casserole.
In a large mixing bowl, crack all 12 eggs and beat them vigorously for about 1 minute until well combined and slightly frothy. Add the cottage cheese and stir until fully incorporated—I find that using a quality cottage cheese like Good Culture prevents the casserole from becoming watery and gives it a creamier texture throughout. The eggs and cottage cheese mixture will look slightly textured, which is perfect.
Add the sautéed vegetables from Step 2 to the egg and cottage cheese mixture, stirring gently but thoroughly to distribute them evenly. Fold in the chopped green onions and taste the mixture, adjusting salt and pepper as needed—remember that you already seasoned the vegetables, so go easy and taste before adding more. Spray a 9x13-inch baking pan with cooking oil or butter to prevent sticking.
Pour the entire egg mixture into the prepared 9x13-inch pan, distributing it evenly. Place in the preheated 375°F oven and bake for 40-45 minutes. The casserole is done when the center is set but still slightly jiggly when gently shaken (it will continue cooking slightly from residual heat), and the top is golden brown. If the top browns too quickly before the center is cooked, loosely tent with foil for the remaining baking time. I always check at 35 minutes to monitor the browning, as every oven varies slightly.