With a sharp knife, slice the squash in half. If the squash is too tough, puncture in several places forming a dotted line around the squash. Microwave for 3-5 minutes to soften. Allow to cool before cutting in half.
Scoop out the seeds, brush with oil, and sprinkle with salt, and pepper. Bake for 40-45 minutes, or until a fork can easily pierce the skin.
In a pan over medium heat, add the oil, garlic, and onions, and sautè until onions are translucent.
Add the cherry tomatoes, salt, and pepper and simmer until they are cooked and begin to become softened.
Remove squash from the oven, with a fork pull at the edges to produce that stringy “spaghetti” quality. Add the squash to the tomato mixture and mix in the pan.
Add mixture back to the hollowed out spaghetti squash halves. Top with mini mozzarella balls ans basil.
Bake an additional 5-10 minutes, or until cheese melts.