Use a fork to puncture the spaghetti squash in a straight line running lengthwise from one end to the other.
Microwave the whole squash for approximately 2 minutes to make it easier to cut. Handle it carefully after heating, as the exterior may be hot.
With a sharp knife, carefully cut the squash lengthwise along the line of fork holes. Keep the stem intact, which helps preserve longer squash strands.
Use a spoon to remove and discard the seeds from both halves, leaving the interior cavities clean.
Preheat the air fryer to 360°F (182°C).
Coat the exposed flesh of each squash half with olive oil, then season with salt and freshly ground black pepper.
Arrange the halves in the air fryer basket with sufficient space between them so they do not overlap.
Air fry for 22–25 minutes, or until the squash flesh is tender.
While the squash cooks, place the cottage cheese, Parmesan, mozzarella, minced garlic, Italian seasoning, and crushed red pepper flakes in a medium bowl.
Stir thoroughly until the cheeses, seasonings, and garlic are evenly incorporated.
When the squash is tender and lightly browned, distribute the prepared cheese mixture evenly over the interior of each half.
Raise the air fryer temperature to 400°F (204°C). Return the squash to the air fryer and cook for another 3–5 minutes, until the cheese has fully melted and developed a golden surface.
Carefully transfer the hot squash halves from the air fryer and allow them to rest for about 1 minute.
Finish with torn or chopped fresh basil and serve the cottage cheese spaghetti squash while warm.