Preheat oven to 350 degrees Fahrenheit. Bring a pot of salted water to a boil. Trim ends off squash, then boil whole until barely tender, about 10 minutes. Halve lengthwise and scoop out centers. Chop up the centers with the spinach.

In a heavy saucepan, melt the butter. Sauté green onions until wilted, then whisk in flour to make a roux. Whisk milk in slowly, stirring continually, then cook until thickened.

Add spices to thickened sauce, then mix in the spinach/squash mixture. Spoon mixture into the squash shells on a baking sheet, then top with cheese and bacon. Bake for 15-20 minutes.