You must cut the spaghetti squash in half. Folks, don't microwave the whole squash or it might explode! Yes, people have exploded their squash when cooking the whole dang thing in the microwave. No joke, just google it.
So not only should you cut it in half, you can take further precautions and help it cook more evenly by poking holes through the middle of the squash with a fork before you microwave it. Also, cooking times will vary depending on the size of the squash.