Preheat oven to 350°F. Gather your yellow squash cut into discs, sliced yellow onion, shredded cheddar, shredded Parmesan, and minced garlic cloves.
In a large skillet, melt salted butter and add yellow onion and ¼ teaspoon salt over medium heat until tender and starting to caramelize, about 6 minutes.
Add squash and cook until 'al dente' but not too soft, about 5 minutes.
Add minced garlic, cook for 2 minutes until fragrant.
Transfer cooked veggies to casserole dish (I used a 3-quart casserole dish).
Beat eggs with milk, fresh parsley, remaining salt, black pepper, and red pepper flakes, and pour egg mixture over the squash in the casserole dish.
Add half the crackers and the shredded cheddar to a bowl. Mix to combine.
Stir in the cracker and cheese mixture into the casserole dish with the squash.
Top the casserole with the remaining crackers.
Sprinkle over the shredded Parmesan.
Bake the casserole for 45 minutes.