Turn your oven to 400. Slice off the top and bottom (stem and blossom ends) of your squash, and then slice the rest into rings (4-5 per squash). Paint both sides with oil, lightly sprinkle with salt and pepper, and then bake for 25-30 minutes until the squash shreds easily with a fork. Pull squash "noodles" away from the rind and set aside.
Brown your meat in a large skillet, breaking apart with a wooden spoon. Once mostly cooked, add the spices and salt.
Stir the chopped tomatoes, green pepper, jalapeño and diced onion into the ground meat and spices. Stir and warm through for a few minutes, then remove from heat.
Lightly grease a 9x13 casserole/baking dish. Add in the spaghetti squash noodles and everything from skillet. Mix well.
In a bowl, whisk together the eggs, salsa and about 2/3rds of your cheese. Pour over top of the casserole.
Sprinkle the remaining cheese on the top, and cover with tinfoil. Bake for 1 hour, remove tinfoil and bake for 15 more minutes. Allow to cool slightly, and serve warm.