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Preheat the Oven: Heat your oven to 375°F (190°C).
Sauté the Aromatics: In a large skillet, cook the diced onion and minced garlic over medium heat until softened (about 3 minutes).
Add and Cook the Jalapenos: Add the diced jalapenos and cook for an additional 2 minutes, allowing their flavors to release.
Make the Roux: Stir in the all-purpose flour and cook for 1 minute to create a roux. This will thicken the sauce later.
Whisk in the Liquids: Gradually add the beef broth and heavy cream to the skillet, whisking constantly to ensure no lumps form.
Simmer and Thicken: Bring the mixture to a simmer and cook until it thickens to your desired consistency.
Incorporate the Cheesy Brisket Filling: Stir in the shredded brisket, cheddar cheese, Monterey Jack cheese, dried thyme, salt, and pepper. Let everything heat through and combine well.
Assemble the Pot Pie: Roll out one pie crust and use it to line a 9-inch pie dish. Pour the prepared brisket filling into the lined pie dish.
Top with Second Crust and Seal: Roll out the second pie crust and place it on top of the filling. Crimp the edges of the two crusts together to seal the pot pie. Cut a few slits in the top crust to allow steam to vent.
Bake until Golden Brown: Place the pot pie in the preheated oven and bake for 35-40 minutes, or until the crust is golden brown and the filling is bubbly.
Serve and Enjoy: Let the pot pie cool slightly before serving. Enjoy this delicious and comforting dish!