Preheat oven to 375 degrees.
Take the crust out of the freezer and let sit on the counter for 3-5 minutes.
Pierce the bottom of the crust with a fork about 5 times (to keep the crust from bubbling up).
Bake for 15 minutes then set aside. Lower the oven temperature to 350 degrees.
Heat the oil in a large skillet over medium heat.
Add the garlic and shallots and cook until fragrant, about 30 seconds.
Remove to a plate and add the asparagus to the pan.
Cook for 3 minutes until slightly tender, then toss in the mushrooms and thyme. Cook for another 3-5 minutes until tender.
Add the shallots and garlic back in to the pan and remove the asparagus on to the plate.
In a medium bowl, whisk the eggs and milk.
Season with salt, pepper, and red pepper flakes.
Fold in the cheese, chives, mushroom and shallot mixture and stir until everything is incorporated.
Pour in to the partially baked crust, then add the asparagus spears on top, one at a time in an even layer.
Sprinkle on the feta cheese. Bake for 50-55 minutes until set.
Let cool slightly then top with extra feta, chives, pesto, arugula, avocado, or any other toppings you'd like. Enjoy!