Prepare the spaghetti squash by slicing off both ends of the squash with a sharp knife. Stand the squash up on one of the cut ends and slice the squash in half lengthwise, doing one side at a time.
Clean out the seeds and insides of each half of the squash by scrapping with a metal spoon.
In a glass baking dish, place the squash halves cut side down. Pour in the water so that it goes up about 1/2-1 inch on the side of the squash.
Cover tightly with clear plastic wrap
Cook the squash in the microwave for 10-15 minutes. The squash is done when the skin is soft and dents in easily.
Remove the squash from the microwave and shred with a fork. Top with your favorite toppings.