With a sharp knife, slice the squash in half lengthwise (if the squash is too tough, puncture in several places, forming a perforated line around the squash. Microwave for 3–5 minutes to soften, then allow to cool before cutting in half). Scoop out the seeds, then place the squash halves cut-side up on a baking sheet. Drizzle the cut sides with olive oil and season with salt and pepper, then use a brush to distribute the seasonings evenly.
3. Step
Bake the squash for 40-45 minutes, or until a fork can easily pierce the skin.
4. Step
Make the filling: Heat the olive oil in a large pan over medium heat, then add the garlic and onion and sauté until the onion is translucent, about 5 minutes. Add the cherry tomatoes, salt, and pepper and simmer until the tomatoes are softened and saucy.
5. Step
Remove the squash from the oven and use a fork pull the flesh into stringy "spaghetti." Add the squash to the pan with the tomato mixture and toss well to combine.
6. Step
Add the squash and tomato mixture to the hollowed-out spaghetti squash halves. Top with the mini mozzarella balls and basil.
7. Step
Bake for 5–10 minutes, or until the cheese melts.
8. Step
Garnish with more basil and serve warm directly in the squash halves.