Preheat the oven to 400F. Slice the spaghetti squash in half lengthwise, scoop out the seeds, and place the halves cut-side-down on a large baking sheet. Bake until a fork can easily pierce the shell of the squash, about 45 to 60 minutes. (For detailed pictures, see this post.)
In a large skillet or dutch oven over medium heat, saute the onion and garlic in coconut oil for 5 minutes, until tender. Add the broccoli and zucchini, and a splash of water to help prevent sticking, then cover and allow the vegetables to cook until tender, about 10 to 15 minutes. Remove the lid and stir well, making sure that any added water has evaporated. Stir in the marinara sauce and spinach, and cook until the spinach has wilted and the marinara sauce is heated through.
You can serve these marinara coated vegetables as is, but for a truly comforting dish, I like to add a crisp and bubbly cheese topping. If your broiler is located at the top of your oven, you can simply sprinkle the cheese over the top of your large skillet and place it in the oven to broil for 2 to 3 minutes, until the cheese is lightly browned.
If your broiler is on the bottom of your oven, like mine is, you may want to divide the vegetable mixture into individual oven-safe dishes so that they more easily can fit under the broiler. Sprinkle each dish with cheese, then broil for 2 to 3 minutes until the top is melted and lightly golden. Serve warm.