Meanwhile, preheat the oven to 375 degrees F (190 degrees C). Grease the bottom of a 9×13-inch baking dish.
Place 6 tortillas into the prepared baking dish. Spread 1/3 of the salsa on top of the tortillas. Spread 1/2 of the meat mixture evenly over the salsa. Sprinkle with 1/2 of the green onions. Drop 1/2 of the sour cream randomly over the green onions. Top with 1/2 cup Cheddar and 1/2 cup Monterey Jack cheese. Repeat layers. Top with 6 tortillas, spread with remaining salsa, and sprinkle with remaining cheese.
Bake in the preheated oven until golden brown on top and cheeses are melted throughout the layers, 30 to 45 minutes.
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