Preheat oven to 375ºF. Grease a 9×13 inch baking pan.
Place olive oil in a deep saute pan over medium-high heat. Once the oil is hot, place onions in the pan.
When the onions start to become translucent, add the garlic, butternut squash, yukon potatoes, and zucchini noodles to the pan. Saute for about 2-3 minutes.
Add in the frozen peas, and cook until the peas are no longer frozen (about 2 minutes).
Turn of the heat and mix in the shredded chicken breast.
Add in the milk, cheese, thyme, salt, and pepper and stir until everything is evenly distributed.
Pour everything into the baking dish and bake for about 25 minutes, or until the squash and potatoes can be easily pierced. Start checking the dish at about 20 minutes. The dish may be ready sooner, depending on your oven.
Remove from oven, and drain excess broth. The zucchini releases a lot of water as it is baking. The broth is quite tasty, so save it for other dishes if you like!