Bake spaghetti squash in 9x13-inch glass baking dish, as you would bake a butternut squash. (Leave oven on...as you will bake this again for a few minutes after mixing it all together!) This takes about an hour, so plan accordingly. You can poke holes in the squash and microwave it for about 15-20 minutes if you are in a time crunch, but I don't think the "spaghetti" part turns out as well when cooked in the microwave. My opinion!
In the mean time, chop broccoli heads, carrots and red pepper. Place in microwavable dish with 1/4 cup of water and cover with plastic wrap. Cook for 5 minutes.
Remove squash (carefully) from baking dish and rinse out the baking dish.