Preheat oven to 350 degrees F (175 degrees C).

Bring a pot of water to a boil; add squash and cook until squash can be easily pierced with a fork, 10 to 15 minutes. Allow squash to cool until easily handled, about 5 minutes.

Cut off one end of squash and scoop meat and seeds out of the center, leaving enough meat intact so squash will still maintain its shape. Set the scooped meat aside.

Place bacon in a large skillet and cook over medium-high heat, turning occasionally, until evenly browned and extra crispy, about 10 minutes. Drain bacon slices on paper towels, reserving about 1/4 teaspoon bacon grease in the skillet.

Cook and stir onion and garlic in the bacon grease over medium heat until onion is translucent, 5 to 10 minutes. Add water, beef bouillon, squash meat, and cayenne pepper to onion mixture; cook until liquid is reduced by about 2/3, about 5 minutes.

Mix Cheddar cheese into broth mixture until cheese is melted completely, 2 to 3 minutes. Add bread crumbs and stir until mixture is the consistency of wet stuffing. Fill squash with stuffing; season with salt and pepper. Place squash in a baking dish.

Bake in the preheated oven until stuffing is crisp, 30 to 45 minutes.