Preheat the air fryer to 375°F. Lightly spray the cut sides of the spaghetti squash with olive oil spray and season with a pinch of salt and pepper. Place the halves cut-side down on a baking sheet and roast in a 375°F oven for 35 to 40 minutes until the flesh shreds easily with a fork.
While the squash cooks, set up a breading station. Mix the panko breadcrumbs, grated Parmesan, Italian seasoning, salt, and pepper in a shallow bowl. Dip each eggplant round first in the beaten eggs, then coat it evenly in the breadcrumb mixture.
Lightly spray both sides of the breaded eggplant with olive oil spray. Arrange the slices in a single layer in the air fryer basket, working in batches if needed. Air fry at 375°F for 12 to 14 minutes, flipping halfway, until the coating is golden and crisp.
Warm the marinara sauce in a small saucepan or microwave. Once the squash is done, shred the flesh into strands with a fork and divide it among four plates.
Top each portion of squash with several pieces of crispy eggplant. Spoon marinara sauce over the eggplant, sprinkle with shredded mozzarella, and return the plates to the air fryer for 1 to 2 minutes until the cheese melts. Finish with fresh basil leaves.