Place the whole spaghetti squash on a microwave-safe plate. Using a sharp fork, carefully poke the squash about 8-10 times all around. This allows steam to escape during the initial microwave and prevents it from exploding. Microwave the squash for 3-4 minutes to soften it slightly, making it easier and safer to cut.
Carefully remove the squash from the microwave; it will be hot. Place it on a cutting board and slice it in half lengthwise. Using a spoon, scoop out and discard the seeds and fibrous strands from both halves. In a microwave-safe dish, add 1/4 cup of water, then place the squash halves face down into the water. Cover the dish tightly with plastic wrap to create a steaming environment.
Microwave the covered squash for 6-10 minutes, or until the flesh is very tender when pierced with a fork. Cooking time will vary based on your microwave's wattage and the size of the squash. Carefully remove the plastic wrap, being mindful of the hot steam escaping. I like to let it sit for a minute or two before uncovering to continue steaming slightly. Use a fork to gently scrape the cooked flesh from the shell, creating spaghetti-like strands.
Transfer the spaghetti squash strands to a serving dish. Add the butter, salt, and freshly ground black pepper to taste. Toss gently until the butter is melted and evenly distributed. I always recommend using freshly ground black pepper for a more pungent aroma and flavor. Serve immediately as a delicious and healthy side dish or base for your favorite sauce.