Preheat oven to 350°F (175°C). Lightly grease a 9x13-inch baking dish.
In a large skillet, sauté the squash and onion over medium heat until soft and most of the moisture is gone. Let cool slightly.
In a large bowl, mix the cooked squash mixture with eggs, sour cream, shredded cheese, salt, and pepper until well combined.
Spread the mixture evenly in the prepared baking dish.
In a small bowl, mix the crushed crackers with melted butter. Sprinkle evenly over the top of the casserole.
Bake for 30–35 minutes, until the top is golden and edges are bubbling. Let rest a few minutes before serving.