Prepare the Squash: Start by cooking the spaghetti squash. For the oven method, preheat your oven to 400°F (200°C). Slice the squash lengthwise and scoop out the seeds and stringy center. Season the cut sides with a bit of salt and pepper, then place them cut-side down on a baking sheet. Roast for about 50–60 minutes, or until the flesh is fork-tender.
Microwave method: Poke several holes in the squash using a knife. Place it on a microwave-safe plate and microwave for 7–9 minutes, or until the skin yields slightly when pressed. Let it cool, then slice, remove seeds, and proceed.
Shred the Squash: Once the squash is cool enough to handle, use a fork to scrape out the flesh into long, spaghetti-like strands. Measure 2 cups and set aside for later.
Sauté the Aromatics and Veggies: In a medium skillet, heat the olive oil over medium-low heat. Add the shallots, garlic, red onion, celery, and carrots, and cook for 5 minutes, stirring occasionally, until the vegetables start to soften and become fragrant.
Add Broccoli and Zucchini: Toss in the broccoli florets and zucchini. Season with a pinch of salt and freshly ground black pepper. Stir well and cook for another 3–4 minutes, allowing the veggies to become tender-crisp.
Simmer with Sauce: Pour in the marinara sauce and raise the heat to medium. Simmer for 3–5 minutes, stirring occasionally, until everything is heated through and the vegetables are coated in the sauce.
Combine with Spaghetti Squash: Mix in the spaghetti squash strands and the grated Pecorino Romano. Stir everything together gently and let it warm through for about 1 minute. Adjust seasoning as needed.
Assemble and Melt Cheese: Spoon the mixture into two individual oven-safe dishes, or use the squash shells as rustic serving bowls. Top each portion with half of the fresh mozzarella. Broil for 1–2 minutes (or bake at 425°F/220°C for 5 minutes) until the cheese melts and starts to bubble.