Heat grill pan over medium heat.
While pan is heating up, toss the zucchini and squash with the olive oil, thyme, salt and pepper.
Place veggies on grill pan and cook about 2-3 minutes per side, until starting to soften and grill marks are present. Remove vegetables from heat and set aside.
Place 1 tortilla (2 if using a double grill pan) on grill pan for 1 minute. Reduce heat to medium low. Using tongs, flip it over and layer vegetables, onion, cheese and basil on one half of tortilla. Fold over and place something heavy on top to weigh it down (small pan filled w/ water, a brick covered in foil, cooking weight). Cook 2-3 more minutes until cheese is melted.
Serve immediately.