Philly-Cheesesteak Shepherd's Pie with Spaghetti Squash Topping

Marinate the Steak: Whisk together the beer, extra-virgin olive oil, minced garlic, 2 dashes of Worcestershire sauce, fresh thyme sprigs, red pepper flakes, salt, and black pepper in a bowl. Pour into a resealable plastic bag. Add the steak, ensuring it's well coated with the marinade. Squeeze out any excess air and seal the bag. Refrigerate to marinate for at least 8 hours, or preferably overnight. (8+ hours)

Prepare the Steak: Remove the steak from the marinade, shaking off any excess. Discard the remaining marinade responsibly. (5 minutes)

Grill the Steak: Preheat an outdoor grill to medium-high heat and lightly oil the grate. Cook the steaks on the preheated grill until they are firm and reddish-pink inside, approximately 3 to 4 minutes per side. An instant-read thermometer inserted into the center should read 130°F (54°C) for medium-rare. Let the steak rest, then cut it into 1x1/2-inch strips. (15 minutes)

Roast the Spaghetti Squash: Preheat your oven to 350°F (175°C). Place the spaghetti squash halves, cut-side down, on a rimmed baking sheet. Pour enough water into the baking sheet to reach about 1/4-inch up the sides of the squash. (5 minutes)

Bake the Squash: Bake in the preheated oven until the squash is tender, about 30 minutes. Remove from the baking sheet and allow to cool until you can easily handle it. Scoop out and discard the seeds, then shred the squash meat into a bowl using a fork. (45 minutes)

Prepare the Squash Topping: Mix the beaten egg into the shredded spaghetti squash. In a separate bowl, whisk together the 1/4 cup flour, garlic powder, onion powder, salt, and black pepper. Mix this dry mixture into the squash mixture until well combined. (10 minutes)

Sauté the Vegetables: Heat olive oil in a large skillet over medium heat. Add the sliced yellow onion, chopped red bell pepper, and chopped yellow bell pepper. Cook and stir until the vegetables begin to brown, about 5 to 10 minutes. (10 minutes)

Create the Cheesesteak Filling: Add the low-sodium beef broth, 4 dashes of Worcestershire sauce, and the remaining fresh thyme sprig to the skillet with the vegetables. Bring the mixture to a simmer. Slowly stir in 1 tablespoon of flour until the sauce thickens, adding more flour if needed. Stir in the steak strips and remove from the heat. (10 minutes)

Assemble the Pie: Spray a 9-inch square casserole dish with cooking spray. Add the beef mixture to the dish, spreading it evenly. Carefully spread the squash mixture over the steak filling, creating an even topping. (10 minutes)

Bake and Finish: Bake in the preheated oven for 30 minutes. Sprinkle the shredded Swiss cheese evenly over the squash layer. Increase the oven temperature to 425°F (220°C) and continue to cook until the cheese begins to brown and bubble, checking every 5 minutes, about 15 minutes. (45 minutes)

Let rest for 10 minutes before serving.