Preheat your oven to 425 F and line a baking sheet with parchment paper for easy cleanup afterwards.
Carefully cut your spaghetti squash in half lengthwise using a very sharp large chef’s knife, scoop out the seeds (I use an ice cream scoop to make this easier) and place, cut side up, on your baking sheet.
Brush both insides lightly with oil and season lightly with sea salt and pepper. Flip your squash cut side down onto your baking sheet and roast for 30-40 minutes.
Once the squash is finished roasting, remove from the oven and carefully flip them back up like a boat.
Use a fork to lightly scrape and loosen the 'spaghetti' strands from the inside of each squash.
Sprinkle evenly with your Italian seasoning, garlic, and crushed pepper flakes.
Add 1/2 cup of marinara sauce into each squash boat and top evenly with mozzarella.
Sprinkle each with 1 Tablespoon of parmesan cheese.
Return to the oven, and roast for 10-15 minutes, or until the cheese is melted and begins to brown.
Allow to cool for a few minutes, then garnish with fresh basil and serve.