Preheat your oven to 350°F (175°C). Grease a 2-quart baking dish.
In a large skillet, heat the olive oil over medium heat. Add the sliced squash and chopped onion. Sauté for about 5-7 minutes until the squash is tender and the onion is translucent.
Remove the skillet from heat and let the mixture cool slightly.
In a large bowl, combine the sautéed squash and onion with salt, black pepper, cheddar cheese, crushed crackers, sour cream, beaten eggs, garlic powder, and thyme. Mix until well combined.
Pour the mixture into the prepared baking dish and spread it evenly.
Bake in the preheated oven for 30-35 minutes, or until the top is golden brown and the casserole is set.
Let it cool for about 10 minutes before serving.