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Step 1
Add 1 cup water to a 6-quart Instant Pot®, then put the rack in the bottom with the handles going up the sides. Deeply pierce the squash all over 12 to 16 times with a fork, then place on the rack (if needed, trim the stem so the squash fits comfortably in the pot, but be careful not to cut into the squash itself).
Step 2
Follow the manufacturer's guide for locking the lid and preparing to cook. Set to pressure cook on high for 12 minutes (see Cook's Note).
Step 3
Meanwhile, add the canned tomatoes to a medium bowl and use your hands to lightly crush the tomatoes. Set aside.
Step 4
After the pressure-cook cycle is complete, follow the manufacturer's guide for quick release and wait until the quick-release cycle is complete. Being careful of any remaining steam, unlock and remove the lid. Use 2 kitchen towels to remove the rack and squash to a cutting board. Carefully pour the water out of the pot. Allow the squash to cool slightly while you prepare the marinara sauce.
Step 5
Set the pot to high saute and allow it to heat up for 2 minutes. Add 2 tablespoons of the oil, then add the onions and a large pinch of salt. Cook, stirring occasionally, until the onions are softened and starting to brown lightly, 6 to 8 minutes. Add the garlic and a pinch of red pepper flakes and cook, stirring frequently, until the garlic is softened, 2 to 3 minutes. Stir in the reserved tomatoes and a large pinch of salt and bring to a strong simmer; cook, stirring occasionally, until the sauce is reduced slightly and thickened, about 10 minutes. Season with additional salt and red pepper flakes if needed.
Step 6
While the sauce is reducing, remove the squash from the rack and split it in half lengthwise. Use a spoon to remove the seeds, then use a fork to scrape the strands of squash from the inside of the skin.
Step 7
Transfer the squash to a large platter and stir in the remaining 2 tablespoons oil, 1 teaspoon salt and red pepper flakes to taste. Season with more salt if needed, then top with the hot marinara sauce. Sprinkle with the Parmesan and basil.