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Heat the oven to 400°. Grease a 9x13" (3 quart) baking dish with avocado oil or coconut oil spray (if freezing, see notes for directions).
Trim the top of the spaghetti squash off (this will cut off the stem so you don't have to cut through it later). Cut the squash in half lengthwise and scoop out and discard the seeds. Coat the cut sides of the squash in a thin layer of avocado oil and season with salt and pepper. Place cut-side down on a plate or dish and cover with plastic wrap with a small vent somewhere along the rim. Microwave for 8-12 minutes (you might have to microwave them separately depending on the size of your microwave), or until the shell is soft to the touch. Set aside to cool (careful, plate will be hot).
Meanwhile, heat 2 tablespoons avocado oil in a large, deep skillet or Dutch oven over medium-high heat. Peel and dice the onion and saute in the oil with 1/2 teaspoon salt until softened, stirring occasionally, about 3-4 minutes.
While the onion cooks, chop the pepper into bite-sized chunks, discarding the seeds. Add to the onion along with 1/2 teaspoon salt and saute until slightly softened, stirring occasionally, about 4-5 minutes.
Add the ground beef to the pan with 1/2 teaspoon salt and break it up into smaller and smaller chunks until it's browned, about 8 minutes. Turn off the heat and set the pan aside to cool.
In a large bowl, whisk the eggs, salsa, cumin, chili powder, garlic powder, paprika, onion powder and 1/2 teaspoon each salt and black pepper.
Use a fork to scrape out the spaghetti squash "noodles" and add to the bowl (hold the squash with a towel if it's still too warm). Add the veggies and beef and stir everything together until well-blended. Be sure to break up and spread out the clumps of squash noodles.
Pour into the greased pan and bake for 50-60 minutes, until set and browned around the edges. Let cool for 20 minutes, add toppings (see notes for ideas) and serve.