Pre-heat the oven to 375° F.
Carefully slice the spaghetti squash in half. I find it helps to first slice off the end with the stem, because it's near impossible to slice through.
Drizzle 1/2 tablespoon of olive oil on each halve.
Sprinkle with kosher salt and ground black pepper.
Bake in the oven for 30 minutes.
While the squash bakes, heat 1 tablespoon of olive oil in a skillet (cast iron if you've got one) over medium heat.
Add the onion, jalapeño, and bell pepper.
Simmer until the onions are translucent, stirring often, approx. 5 minutes.
Add the beans and the olives.
Add all of the spices, and stir until everything is evenly coated.
Add the tomato sauce, mix, and bring the heat to low. Let it simmer until the squash has finished baking.
Once the squash is ready, remove from the oven and allow to cool enough to handle (or handle while wearing oven mitts, if you're impatient like me).
Drag a fork across the inner flesh of the squash to string it. Do this until you're close to the outer skin of the squash - but definitely leave some room in between.
Empty the spaghetti squash into the skillet and mix thoroughly.
Carefully spoon the spaghetti squash mixture back into the squash halves, or "boats" as everyone likes to call them.
Sprinkle the shredded cheese on the tops of the boats evenly and put back in the oven for approx. 8 - 10 minutes or until the cheese fully melts.
Top with a dollop of plain Greek yogurt or sour cream and garnish with sliced scallions before serving.