Preheat Oven: Set your oven to 375°F (190°C).
Cook Aromatics: In a large skillet or Dutch oven, heat a tablespoon of oil if needed. Sauté the chopped onion and minced garlic over medium heat until softened and fragrant, about 3 minutes.
Add Jalapeños: Stir in the chopped jalapeños (without seeds for less heat) and cook for another 2 minutes to bring out their flavor.
Make the Roux: Sprinkle flour over the vegetables and stir constantly for 1 minute to form a roux that will thicken the filling.
Add Liquids: Slowly whisk in the beef broth and heavy cream, stirring continuously to prevent lumps. Continue whisking until smooth.
Simmer and Thicken: Let the mixture simmer gently, stirring occasionally, until it thickens to your liking.
Combine Filling: Lower the heat. Mix in the shredded brisket, Cheddar, Monterey Jack cheeses, dried thyme, salt, and pepper. Stir until the cheese melts and the filling is evenly combined and heated through. Remove from heat.
Assemble Pie: Press one pie crust into a 9-inch pie dish, shaping it along the bottom and sides. Pour the brisket filling evenly into the crust. Cover with the second crust, sealing edges by crimping. Cut a few slits in the top crust to vent steam.
Bake: Place the pie on a baking sheet and bake for 35-40 minutes until the crust is golden and the filling bubbles.
Rest and Serve: Let the pie cool for 10-15 minutes to allow the filling to set before slicing. Enjoy this rich, hearty dish!
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