Reduce the heat to a simmer and allow the squash to cook for 30 minutes.

Remove the squash from the saucepan and allow it to cool enough to handle.

Cut off the stem and cut the squash in half lengthwise.

Scoop out and discard the seeds, being careful not to cut away much of the flesh of the squash.

Scrape the squash's flesh into strands into a bowl and discard the shell. Set aside.

Place the pine nuts in a large skillet over medium-high heat.

Cook, tossing continuously, until the pine nuts are lightly browned. Remove the pine nuts to a bowl and set aside.

Add the olive oil to the pan over medium-high heat and add the flour.

Whisk continuously for about 1 minute, adjusting the heat so the flour doesn't brown.

Ad the milk, the thyme, and the salt, and whisk for 1 minute, or until the sauce begins to thicken.

Add the goat cheese, whisking continuously until the goat cheese is melted and the sauce is completely smooth.

Add the spaghetti squash, the mozzarella, and the pepper and reduce the heat to medium.

Using tongs, gently fold the squash into the sauce for about 1 minute until heated through. The mozzarella will not melt completely.

Serve topped with the pine nuts.