Place squash skin side up (one half at a time), on microwave-safe dish; cover with microwave-safe plastic wrap. Microwave on HIGH 10-12 min, until tender. Let stand 10-15 min, until cool enough to handle. Carefully remove wrap to avoid steam.
Run tines of fork lengthwise over squash to loosen spaghetti-like strands; scoop out strands; set aside.
While squash microwaves, heat large stockpot on MEDIUM-HIGH; add oil and mirepoix. Cook, stirring occasionally, about 3 min, until softened. Add garlic and mushrooms; cook, stirring, about 2 min, until vegetables start to brown. Stir in tomatoes; simmer 8-10 minute.
Add vegetable stock; simmer 20 minutes. Stir in squash and thyme; season to taste with salt and pepper. Simmer 5 minute Add spinach; stir 1-2 min until wilted.