Step 1

Preheat oven to 400 degrees F. Line a baking sheet with parchment paper.

Step 2

Place squash cut-side down on the prepared pan. Bake until tender, 50 minutes to 1 hour. Turn over and let cool slightly. Scoop the flesh into a food processor and add salt. Puree until smooth. Measure out 2 cups of puree (reserve any remaining squash for another use). Set aside.

Step 3

Meanwhile, combine oil and onion in a medium saucepan. Cover and cook over medium heat, stirring often, for 10 minutes. Uncover and continue cooking until the onion is very soft and browned, 8 to 10 minutes more, reducing the heat and adding 1 tablespoon water at a time, as needed, if the onion begins browning too quickly. Stir in chili powder and chipotle (or cayenne). Remove from heat, cover and let stand for 10 minutes.

Step 4

When the squash is done, reduce oven temperature to 350 degrees. Coat a medium cast-iron skillet (10-inch) with cooking spray.

Step 5

Toss Cheddar and Monterey Jack in a large bowl. Stir 1 cup of the cheeses into the reserved squash puree. Spread about half of the remaining cheese in the prepared pan. Top with the squash. Spread half of the caramelized onions over the squash. Top with the remaining cheese and onions.

Step 6

Bake until the cheese is melted and bubbling along the edges, about 20 minutes. Let cool for 10 minutes. Top with pico de gallo (or salsa), cilantro and pepitas.