Cut squash in half length-wise. This can be pretty difficult since their skin is so tough, so take it slow and use a sharp knife. Alternatively, you can poke it a few times and microwave it for 4-5 minutes to soften it slightly before cutting.
Scoop out the seeds and inner pulp with a spoon.
Place the halves face down on a baking sheet or pan. Bake 35-40 minutes until squash is tender. When the squash is ready to take out of the oven, set aside and let rest on wire rack until cool enough to handle.
The marinara can be cooked while the squash cools, but if you want to let it simmer for longer, feel free to start it while the squash is in the oven.
Heat 2 tbs olive oil over medium-high heat.
Add the onion and garlic, along with a pinch of salt and cook until it begins to become tender, about 5 minutes.
Add tomato paste and cook, stirring constantly, for 1 minute.
Add oregano and crushed tomatoes with juices and let simmer at least 10 minutes (longer if desired or if waiting for the spaghetti squash).
Before removing from heat, stir in basil and red pepper flakes and cook for 1 minute.
Once the squash has cooled, scrape the insides with a fork over a large mixing bowl. Be careful not to poke a hole through the skin.
Serve with fresh marinara on top, sprinkled with freshly grated Parmesan, and enjoy!
Notes
A 4 lb spaghetti squash will yield about 5 cups of "pasta."