Preheat oven to 350 degrees F (175 degrees C). Grease a 1-quart casserole dish.
Place a steamer insert into a saucepan and fill with water to just below the bottom of the steamer. Bring water to a boil. Add squash and onion, cover, and steam until squash is tender and easily mashed with a fork, 10 to 15 minutes.
Whisk egg and sour cream together in the prepared casserole dish; add squash, onions, 2/3 the crackers, and 2/3 the Cheddar cheese. Stir with a fork. Cover the squash mixture with remaining Cheddar cheese and crackers.
Bake in the preheated oven until cheese is melted and crackers are lightly browned, about 30 minutes.