Cut the spaghetti squash in half, hot dog style, roast in a 400 degree oven for 50 minutes, allow to cool.
Remove the seeds from the squash, use a fork to remove the meat from the squash, it should comb out like strands of spaghetti. Put these in a bowl and set aside.
Add either roasted or steamed broccoli to the spaghetti squash strands.
Melt the ghee in a medium sauce pan, whisk in the flour, quickly whisk in the milk, add the dry mustard.
Add the cheeses to the sauce pan, turn the heat down a little, and stir often until the mixture turns thick, about 8 minutes.
Pour the cheese sauce over the squash and broccoli, add salt and pepper, and stir until everything is coated with cheese sauce. Sprinkle on red pepper flakes and enjoy!